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Mechanistic Information (mechanistic + information)
Selected AbstractsTn5 as a model for understanding DNA transpositionMOLECULAR MICROBIOLOGY, Issue 5 2003William S. Reznikoff Summary Tn5 is an excellent model system for understanding the molecular basis of DNA-mediated transposition. Mechanistic information has come from genetic and biochemical investigations of the transposase and its interactions with the recognition DNA sequences at the ends of the transposon. More recently, molecular structure analyses of catalytically active transposase; transposon DNA complexes have provided us with unprecedented insights into this transposition system. Transposase initiates transposition by forming a dimeric transposase, transposon DNA complex. In the context of this complex, the transposase then catalyses four phosphoryl transfer reactions (DNA nicking, DNA hairpin formation, hairpin resolution and strand transfer into target DNA) resulting in the integration of the transposon into its new DNA site. The studies that elucidated these steps also provided important insights into the integration of retroviral genomes into host DNA and the immune system V(D)J joining process. This review will describe the structures and steps involved in Tn5 transposition and point out a biologically important although surprising characteristic of the wild-type Tn5 transposase. Transposase is a very inactive protein. An inactive transposase protein ensures the survival of the host and thus the survival of Tn5. [source] Generalized treatment of NMR spectra for rapid chemical reactionsCONCEPTS IN MAGNETIC RESONANCE, Issue 4 2007Matthew D. Christianson Abstract Application of NMR spectroscopy to fast irreversible reactions (t1/2 < 0.7 s) has been hampered by limitations in instrumentation and general methods for modeling the complicated spectra that result. Analytical descriptions of nuclear spin dynamics during fast reactions, first solved by Ernst and coworkers, are limited to first-order reaction kinetics. We demonstrate that numeric methods enable simulation of NMR spectra for fast reactions having any form of rate law. Simulated stopped-flow NMR spectra are presented for a variety of common kinetic scenarios including reversible and irreversible reactions of first and second-order, multistep reactions, and catalytic transformations. The simulations demonstrate that a wealth of mechanistic information, including reaction rates, rate laws, and the existence of intermediates, is imbedded in a single NMR spectrum. The sensitivity of modern NMR instrumentation along with robust methods for simulating and fitting kinetic parameters of fast reactions make stopped-flow NMR an attractive method for kinetic studies of fast chemical reactions. © 2007 Wiley Periodicals, Inc. Concepts Magn Reson Part A 30A: 165,183, 2007. [source] Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessmentENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 3 2010Gerald T. Ankley Abstract Ecological risk assessors face increasing demands to assess more chemicals, with greater speed and accuracy, and to do so using fewer resources and experimental animals. New approaches in biological and computational sciences may be able to generate mechanistic information that could help in meeting these challenges. However, to use mechanistic data to support chemical assessments, there is a need for effective translation of this information into endpoints meaningful to ecological risk,effects on survival, development, and reproduction in individual organisms and, by extension, impacts on populations. Here we discuss a framework designed for this purpose, the adverse outcome pathway (AOP). An AOP is a conceptual construct that portrays existing knowledge concerning the linkage between a direct molecular initiating event and an adverse outcome at a biological level of organization relevant to risk assessment. The practical utility of AOPs for ecological risk assessment of chemicals is illustrated using five case examples. The examples demonstrate how the AOP concept can focus toxicity testing in terms of species and endpoint selection, enhance across-chemical extrapolation, and support prediction of mixture effects. The examples also show how AOPs facilitate use of molecular or biochemical endpoints (sometimes referred to as biomarkers) for forecasting chemical impacts on individuals and populations. In the concluding sections of the paper, we discuss how AOPs can help to guide research that supports chemical risk assessments and advocate for the incorporation of this approach into a broader systems biology framework. Environ. Toxicol. Chem. 2010;29:730,741. © 2009 SETAC [source] Mixture toxicity and gene inductions: Can we predict the outcome?ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 3 2008Freddy Dardenne Abstract As a consequence of the nature of most real-life exposure scenarios, the last decade of ecotoxicological research has seen increasing interest in the assessment of mixture ecotoxicology. Often, mixtures are considered to follow one of two models, concentration addition (CA) or response addition (RA), both of which have been described in the literature. Nevertheless, mixtures that deviate from either or both models exist; they typically exhibit phenomena like synergism, ratio or concentration dependency, or inhibition. Moreover, both CA and RA have been challenged and evaluated mainly for acute responses at relatively high levels of biological organization (e.g., whole-organism mortality), and applicability to genetic responses has not received much attention. Genetic responses are considered to be the primary reaction in case of toxicant exposure and carry valuable mechanistic information. Effects at the gene-expression level are at the heart of the mode of action by toxicants and mixtures. The ability to predict mixture responses at this primary response level is an important asset in predicting and understanding mixture effects at different levels of biological organization. The present study evaluated the applicability of mixture models to stress gene inductions in Escherichia coli employing model toxicants with known modes of action in binary combinations. The results showed that even if the maximum of the dose,response curve is not known, making a classical ECx (concentration causing x% effect) approach impossible, mixture models can predict responses to the binary mixtures based on the single-toxicant response curves. In most cases, the mode of action of the toxicants does not determine the optimal choice of model (i.e., CA, RA, or a deviation thereof). [source] A semimechanistic model predicting the growth and production of the bioenergy crop Miscanthus×giganteus: description, parameterization and validationGCB BIOENERGY, Issue 4 2009FERNANDO E. MIGUEZ Abstract Biomass based bioenergy is promoted as a major sustainable energy source which can simultaneously decrease net greenhouse gas emissions. Miscanthus×giganteus (M.×giganteus), a C4 perennial grass with high nitrogen, water, and light use efficiencies, is regarded as a promising energy crop for biomass production. Mathematical models which can accurately predict M.×giganteus biomass production potential under different conditions are critical to evaluate the feasibility of its production in different environments. Although previous models based on light-conversion efficiency have been shown to provide good predictions of yield, they cannot easily be used in assessing the value of physiological trait improvement or ecosystem processes. Here, we described in detail the physical and physiological processes of a previously published generic mechanistic eco-physiological model, WIMOVAC, adapted and parameterized for M.×giganteus. Parameterized for one location in England, the model was able to realistically predict daily field diurnal photosynthesis and seasonal biomass at a range of other sites from European studies. The model provides a framework that will allow incorporation of further mechanistic information as it is developed for this new crop. [source] Metal-complex formation and DNA interaction of 5, 10,15,20-tetrakis(1-methyl-4-pyridiyl)-porphine: Study of the mechanistic aspectsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 2 2010Sabriye Aydinoglu The macrocyclic porphyrin 5,10,15,20-tetrakis(1-methyl-4-pyridiyl)-porphine is studied in its ability to coordinate Cu(II) even at very low pH values and to interact, as a copper complex, with calf-thymus (CT-DNA). The kinetics and equilibria for metal-ligand complexes formation are spectrophotometrically studied, particularly focussing on the mechanistic information provided by the kinetic approach. The rate constants of complex formation is much lower than that of water exchange at Cu(II); this behavior is ascribed to an equilibrium between two porphyrin populations, only one of them being reactive. Concerning the interaction of the copper,porphyrin complex (D) with CT-DNA, it has been found that the complex binds to G,C base pairs by intercalation while forms external complex with the A,T base pairs. The kinetic results agree with a reaction mechanism that takes into account the slow shuffling from an AT-bound form (DAT) to a GC-bound form (DGC) of the copper complex (D), finally leading to a more stable DGC* intercalated form. Kinetic and equilibrium parameters for the copper complex binding to the nucleic acid are obtained, and the binding mechanism is discussed. A mechanism is proposed where D reacts simultaneously with (G,C) and (A,T) base pairs. The resulting bound forms interconvert according to a "shuffling" process, which involves formation of an intermediate (DGC) form. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 42: 79,89, 2010 [source] The reaction of OH with acetaldehyde and deuterated acetaldehyde: Further insight into the reaction mechanism at both low and elevated temperaturesINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 8 2006Philip H. Taylor The pulsed laser photolysis/laser-induced fluorescence technique has been used to conduct additional measurements of the gas-phase CH3CHO + OH reaction. These measurements were conducted to verify the complex temperature dependence previously observed by the authors and to acquire mechanistic information about the reaction mechanism in the form of primary kinetic isotope effects. Primary kinetic isotope effect measurements at temperatures of 297, 383, 600, and 860 K indicate that H abstraction from the acetyl group dominates that of the methyl group at low to modest temperatures (,600 K) and H abstraction from the methyl group dominates that from the acetyl group at higher temperatures (860 K). A bi-exponential © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 489,495, 2006 [source] Rate coefficients and mechanisms of the reaction of cl-atoms with a series of unsaturated hydrocarbons under atmospheric conditionsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 8 2003John J. Orlando Rate coefficients and/or mechanistic information are provided for the reaction of Cl-atoms with a number of unsaturated species, including isoprene, methacrolein (MACR), methyl vinyl ketone (MVK), 1,3-butadiene, trans -2-butene, and 1-butene. The following Cl-atom rate coefficients were obtained at 298 K near 1 atm total pressure: k(isoprene) = (4.3 ± 0.6) × 10,10cm3 molecule,1 s,1 (independent of pressure from 6.2 to 760 Torr); k(MVK) = (2.2 ± 0.3) × 10,10 cm3 molecule,1 s,1; k(MACR) = (2.4 ± 0.3) × 10,10 cm3 molecule,1 s,1; k(trans -2-butene) = (4.0 ± 0.5) × 10,10 cm3 molecule,1 s,1; k(1-butene) = (3.0 ± 0.4) × 10,10 cm3 molecule,1 s,1. Products observed in the Cl-atom-initiated oxidation of the unsaturated species at 298 K in 1 atm air are as follows (with % molar yields in parentheses): CH2O (9.5 ± 1.0%), HCOCl (5.1 ± 0.7%), and 1-chloro-3-methyl-3-buten-2-one (CMBO, not quantified) from isoprene; chloroacetaldehyde (75 ± 8%), CO2 (58 ± 5%), CH2O (47 ± 7%), CH3OH (8%), HCOCl (7 ± 1%), and peracetic acid (6%) from MVK; CO (52 ± 4%), chloroacetone (42 ± 5%), CO2 (23 ± 2%), CH2O (18 ± 2%), and HCOCl (5%) from MACR; CH2O (7 ± 1%), HCOCl (3%), acrolein (,3%), and 4-chlorocrotonaldehyde (CCA, not quantified) from 1,3-butadiene; CH3CHO (22 ± 3%), CO2 (13 ± 2%), 3-chloro-2-butanone (13 ± 4%), CH2O (7.6 ± 1.1%), and CH3OH (1.8 ± 0.6%) from trans -2-butene; and chloroacetaldehyde (20 ± 3%), CH2O (7 ± 1%), CO2 (4 ± 1%), and HCOCl (4 ± 1%) from 1-butene. Product yields from both trans -2-butene and 1-butene were found to be O2 -dependent. In the case of trans -2-butene, the observed O2 -dependence is the result of a competition between unimolecular decomposition of the CH3CH(Cl)CH(O,)CH3 radical and its reaction with O2, with kdecomp/kO2 = (1.6 ± 0.4) × 1019 molecule cm,3. The activation energy for decomposition is estimated at 11.5 ± 1.5 kcal mol,1. The variation of the product yields with O2 in the case of 1-butene results from similar competitive reaction pathways for the two ,-chlorobutoxy radicals involved in the oxidation, ClCH2CH(O,)CH2CH3 and ,OCH2CHClCH2CH3. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 334,353, 2003 [source] Mechanistic Inferences Derived from Competitive Catalytic Reactions: Pd(binap)-Catalyzed Amination of Aryl HalidesADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 7-8 2008Antonio Abstract Healthy competition: The Pd(binap)-catalyzed amination of aryl halides demonstrates how the results from competitive reactions can be strikingly different from those obtained from study of the separate reactions. We show how the competitive network provides mechanistic information not accessible from study of the reactions separately. [source] Interpretation of the temperature dependence of equilibrium and rate constantsJOURNAL OF MOLECULAR RECOGNITION, Issue 5 2006Donald J. Winzor Abstract The objective of this review is to draw attention to potential pitfalls in attempts to glean mechanistic information from the magnitudes of standard enthalpies and entropies derived from the temperature dependence of equilibrium and rate constants for protein interactions. Problems arise because the minimalist model that suffices to describe the energy differences between initial and final states usually comprises a set of linked equilibria, each of which is characterized by its own energetics. For example, because the overall standard enthalpy is a composite of those individual values, a positive magnitude for ,Ho can still arise despite all reactions within the subset being characterized by negative enthalpy changes: designation of the reaction as being entropy driven is thus equivocal. An experimenter must always bear in mind the fact that any mechanistic interpretation of the magnitudes of thermodynamic parameters refers to the reaction model rather than the experimental system For the same reason there is little point in subjecting the temperature dependence of rate constants for protein interactions to transition-state analysis. If comparisons with reported values of standard enthalpy and entropy of activation are needed, they are readily calculated from the empirical Arrhenius parameters. Copyright © 2006 John Wiley & Sons, Ltd. [source] Probing residue-specific interactions in the stabilization of proteins using high-resolution NMR: A study of disulfide bond compensationJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 6 2010Andria L. Skinner Abstract It is well established that the oxidation state of cysteine residues in proteins is critical to overall physical stability. Disulfide bonds most often impart thermodynamic stability, but in some cases, diminish it. Predicting the circumstances that lead to each outcome is difficult because mechanistic information is lacking. Because the techniques typically used to study protein stability do not provide sufficient detail, high-resolution NMR was used in combination with low-resolution analysis to obtain mechanistic information regarding disulfide bond formation in a model protein. Tm (CD) and Tonset (SLS) for the reduced and oxidized wild type and C104S and C49S mutants were measured. The mutant proteins have altered Tms and Tonsets compared to the reduced wild type, indicating that differences in local interactions of the Cys side chains are important for stability. The NMR spectra clearly show distinct differences in the chemical environment surrounding these Cys residues and the overall tertiary structure. The C49S protein, which is less stable and more aggregation prone than reduced wild type, lacks a hydrogen bond between Y53 and H103. Increased flexibility of the Y53-containing loop is correlated with increased dynamics and unraveling of ,2, which likely leads to edge strand initiated aggregation of the central ,-sheet. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99: 2643,2654, 2010 [source] Thermodynamic and structural aspects of sulfonamide crystals and solutionsJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 12 2009German L. Perlovich Abstract The crystal structures of three sulfonamides with the general structure 4-NH2 -C6H4 -SO2NH-C6H4/3 -R (R,=,4-Et; 4-OMe; 5-Cl-2-Me) have been determined by X-ray diffraction. On the basis of our previous data and the results obtained a comparative analysis of crystal properties was performed: molecular conformational states, packing architecture, and hydrogen bond networks using graph set notations. The thermodynamic aspects of the sulfonamide sublimation process have been studied by investigating the temperature dependence of vapor pressure using the transpiration method. A regression equation was derived describing the correlation between sublimation entropy terms and crystal density data calculated from X-ray diffraction results. Also correlations between sublimation Gibbs energies and melting points, on the one hand, and between sublimation enthalpies and fusion enthalpies at 298 K, on the other hand, were found. These dependencies give the opportunity to predict sublimation thermodynamic parameters by simple thermo-physical experiments (fusion characteristics). Solubility processes of the compounds in water, n -hexane, and n -octanol (as phases modeling various drug delivery pathways and different types of membranes) were investigated and corresponding thermodynamic functions were calculated as well. Thermodynamic characteristics of sulfonamide solvation were evaluated. For compounds with similar structures processes of transfer from one solvent to another one were studied by a diagram method combined with analysis of enthalpic and entropic terms. Distinguishing between enthalpy and entropy, as is possible through the present approach, leads to the insight that the contribution of these terms is different for different molecules (entropy- or enthalpy-determined). Thus, in contrast to interpretation of only the Gibbs energy of transfer, being extensively used for pharmaceuticals in the form of the partition coefficient (log,P), the analysis of thermodynamic functions of the transfer process provides additional mechanistic information. This may be important for further evaluation of the physiological distribution of drug molecules and may provide a better understanding of biopharmaceutical properties of drugs. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:4738,4755, 2009 [source] Ethanol Enhances Taurine-Activated Glycine Receptor FunctionALCOHOLISM, Issue 9 2010Brian T. Welsh Background:, Emerging evidence suggests that taurine acts as a partial agonist on glycine receptors (GlyR) in vitro and in vivo. Ethanol acts as an allosteric modulator on the GlyR producing a leftward shift of the glycine concentration,response curve, with no enhancing effects observed at saturating glycine concentrations. However, to date, no electrophysiological studies have been performed on ethanol modulation of taurine-activated GlyR. Methods:, Wild-type ,1 GlyR, or those bearing a serine-267 to isoleucine replacement (S267I), were homomerically expressed in Xenopus oocytes and voltage clamped at ,70 mV. Ethanol was co-applied with varying concentrations of glycine or taurine and the enhancing effects of ethanol compared. Results:, Ethanol potentiated glycine- and taurine-activated GlyR responses in a concentration-dependent manner. It shifted taurine and glycine concentration,response curves to the left, having no effects at saturating agonist concentrations. Chelation of zinc by tricine decreased ethanol enhancement of taurine-gated GlyR function. The S267I mutation prevented ethanol enhancement of taurine-mediated responses as previously also reported for glycine. Conclusion:, Ethanol modulates taurine activation of GlyR function by a mechanism similar to that of the full agonist glycine. The lack of effect of ethanol at saturating taurine concentrations provides mechanistic information on alcohol actions at the GlyR. [source] The role of low soil temperature in the inhibition of growth and PSII function during dark chilling in soybean genotypes of contrasting tolerancePHYSIOLOGIA PLANTARUM, Issue 1 2007Abram J. Strauss Dark chilling affects growth and yield of warm-climate crops such as soybean [Glycine max (L.) Merr.]. Several studies have investigated chilling-stress effects on photosynthesis and other aspects of metabolism, but none have compared effects of whole-plant chilling (WPC; shoots and roots) with that of aboveground chilling in legumes. This is important because low root temperatures might induce additional constraints, such as inhibition of N2 fixation, thereby aggravating chilling-stress symptoms. Effects of dark chilling on PSII, shoot growth, leaf ureide content and photosynthetic capacity were studied in two soybean genotypes, Highveld Top (chilling tolerant) and PAN809 (chilling sensitive), in experiments comparing effects of WPC with that of shoot chilling (SC). Both treatments inhibited shoot growth in PAN809 but not Highveld Top. Also, WPC in PAN809 caused a decrease in leaf ureide content followed by severe chlorosis and alterations in O-J-I-P fluorescence-rise kinetics, distinct from SC. A noteworthy difference was the appearance of a ,K peak in the O-J-I-P fluorescence rise in response to WPC. These genotypic and treatment differences also reflected in the degree of inhibition of CO2 assimilation rates. The appearance of a ,K peak, coupled with growth inhibition, reduced ureide content, chlorosis and lower CO2 assimilation rates, provides mechanistic information about how WPC might have aggravated chilling-stress symptoms in PAN809. We introduce a model explaining how chilling soil temperatures might trigger N-limitation in sensitive genotypes and how characteristic changes in O-J-I-P fluorescence-rise kinetics are linked to changes in carbon and nitrogen metabolism. [source] Can molecular mechanisms of biological processes be extracted from expression profiles?BIOESSAYS, Issue 12 2001Case study: endothelial contribution to tumor-induced angiogenesis Whereas the genome contains all potential developmental programs, expression profiles permit the determination of genes that are actively transcribed under defined physiological conditions. In this article, the idea of extracting biological mechanisms from expression data is tested. Molecular processes of the endothelial contribution to angiogenesis are derived from recently published expression profiles. The analysis reveals the sensitivity limits of experimental detection of transcriptional changes and how sequence-analytic techniques can help to identify the function of genes in question. We conclude that the transcripts (http://mendel.imp.univie.ac.at/SEQUENCES/TEMS/) found to be up-regulated in angiogenesis are involved in extracellular matrix remodeling, cellular migration, adhesion, cell-cell communication rather than in angiogenesis initiation or integrative control. Comparison with tissue-specific patterns of EST occurrence shows that, indeed, the presumptive tumor-specific endothelial markers are more generally expressed by cell types involved in migration and matrix remodeling processes. This exemplary study demonstrates how bioinformatics approaches can be helpful in deriving mechanistic information from diverse sources of experimental data. BioEssays 23:1159,1175, 2001. © 2001 John Wiley & Sons, Inc. [source] UNRAVELLING THE PATHOPHYSIOLOGY OF COMPLEX REGIONAL PAIN SYNDROME: FOCUS ON SYMPATHETICALLY MAINTAINED PAINCLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 7 2008Gael F Gibbs SUMMARY 1In diseases such as complex regional pain syndrome (CRPS), where neuropathic pain is the primary concern, traditional pain classifications and lesion descriptors are of limited value. To obtain better treatment outcomes for patients, the underlying pathophysiological mechanisms of neuropathic pain need to be elucidated and analysed so that therapeutic targets can be identified and specific treatments developed. 2In the present review, we examine the current literature on sympathetically maintained pain (SMP), a subset of neuropathic pain, within the context of CRPS. Evidence from both human and animal studies is presented and discussed in terms of its support for the existence of SMP and the mechanistic information it provides. 3We discuss three current hypotheses that propose both a site and method for sympathetic,sensory coupling: (i) direct coupling between sympathetic and sensory neurons in the dorsal root ganglion; (ii) chemical coupling between sympathetic and nociceptive neuron terminals in skin; and (iii) the development of a-adrenoceptor-mediated supersensitivity in nociceptive fibres in skin in association with the release of inflammatory mediators. 4Finally, we propose a new hypothesis that integrates the mechanisms of chemical coupling and a-adrenoceptor-mediated supersensitivity. This hypothesis is based on previously unpublished data from our laboratory showing that a histological substrate suitable for sympathetic,sensory coupling exists in normal subjects. In the diseased state, the nociceptive fibres implicated in this substrate may be activated by both endogenous and exogenous noradrenaline. The mediating a-adrenoceptors may be expressed on the nociceptive fibres or on closely associated support cells. [source] | ||||||||||||||||