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Mechanistic analysis of the Saccharomyces cerevisiae kinesin Kar3.

Kar3 is a minus-end-directed microtubule motor that is implicated in meiotic and mitotic spindle function in Saccharomyces cerevisiae. To date, the only truncated protein of Kar3 that has been reported to promote unidirectional movement in vitro is GSTKar3. This motor contains an NH2-terminal glutathione S-transferase (GST) tag followed by the Kar3 sequence that is predicted to form an extended alpha-helical coiled-coil. The alpha-helical domain leads into the neck linker and COOH-terminal motor domain. Kar3 does not homodimerize with itself but forms a heterodimer with either Cik1 or Vik1, both of which are non-motor polypeptides. We evaluated the microtubule-GSTKar3 complex in comparison to the microtubule-Kar3 motor domain complex to determine the distinctive mechanistic features required for GSTKar3 motility. Our results indicate that ATP binding was significantly faster for GSTKar3 than that observed previously for the Kar3 motor domain. In addition, microtubule-activated ADP release resulted in an intermediate that bound ADP weakly in contrast to the Kar3 motor domain, suggesting that after ADP release, the microtubule-GSTKar3 motor binds ATP in preference to ADP. The kinetics also showed that GST-Kar3 readily detached from the microtubule rather than remaining bound for multiple ATP turnovers. These results indicate that the extended alpha-helical domain NH2-terminal to the catalytic core provides the structural transitions in response to the ATPase cycle that are critical for motility and that dimerization is not specifically required. This study provides the foundation to define the mechanistic contributions of Cik1 and Vik1 for Kar3 force generation and function in vivo.

Adenosine Diphosphate↗

Mechanistic differences in RNA-dependent DNA polymerization and fidelity between murine leukemia virus and HIV-1 reverse transcriptases.

We compared the mechanistic and kinetic properties of murine leukemia virus (MuLV) and human immunodeficiency virus type 1 (HIV-1) reverse transcriptases (RTs) during RNA-dependent DNA polymerization and mutation synthesis using pre-steady-state kinetic analysis. First, MuLV RT showed 6.5-121.6-fold lower binding affinity (K(d)) to deoxynucleotide triphosphate (dNTP) substrates than HIV-1 RT, although the two RTs have similar incorporation rates (k(pol)). Second, compared with HIV-1 RT, MuLV RT showed dramatic reduction during multiple dNTP incorporations at low dNTP concentrations. Presumably, due to its low dNTP binding affinity, the dNTP binding step becomes rate-limiting in the multiple rounds of the dNTP incorporation by MuLV RT, especially at low dNTP concentrations. Third, similar fold differences between MuLV and HIV-1 RTs in the K(d) and k(pol) values to correct and incorrect dNTPs were observed. This indicates that these two RT proteins have similar misinsertion fidelities. Fourth, these two RT proteins have different mechanistic capabilities regarding mismatch extension. MuLV RT has a 3.1-fold lower mismatch extension fidelity, compared with HIV-1 RT. Finally, MuLV RT has a 3.8-fold lower binding affinity to mismatched template/primer (T/P) substrate compared with HIV-1 RT. Our data suggest that the active site of MuLV RT has an intrinsically low dNTP binding affinity, compared with HIV-1 RT. In addition, instead of the misinsertion step, the mismatch extension step, which varies between MuLV and HIV-1 RTs, contributes to their fidelity differences. The implications of these kinetic differences between MuLV and HIV-1 RTs on viral cell type specificity and mutagenesis are discussed.

Animals↗

Mechanistic insights into the isochorismate pyruvate lyase activity of the catalytically promiscuous PchB from combinatorial mutagenesis and selection.

PchB from Pseudomonas aeruginosa possesses isochorismate pyruvate lyase (IPL) and weak chorismate mutase (CM) activity. Homology modeling based on a structurally characterized CM, coupled with randomization of presumed key active site residues (Arg54, Glu90, Gln91) and in vivo selection for CM activity, was used to derive mechanistic insights into the IPL activity of PchB. Mutation of Arg54 was incompatible with viability, and the CM and IPL activities of an engineered R54K variant were reduced 1,000-fold each. The observation that position 90 was tolerant to substitution but position 91 was essentially confined to Gln or Glu in functional variants rules out involvement of Glu90 in general base catalysis. Counter to the generally accepted mechanistic hypothesis for pyruvate lyases, we propose for PchB a rare [1,5]-sigmatropic reaction mechanism that invokes electrostatic catalysis in analogy to the [3,3]-pericyclic rearrangement of chorismate in CMs. A common catalytic principle for both PchB functions is also supported by the covariance of the catalytic parameters for the CM and IPL activities and the shared functional requirement for a protonated Glu91 in Q91E variants. The experiments demonstrate that focusing directed evolution strategies on the readily accessible surrogate activity of an enzyme can provide valuable insights into the mechanism of the primary reaction.

Amino Acid Sequence↗

Overexpression and mechanistic characterization of blastula protease 10, a metalloprotease involved in sea urchin embryogenesis and development.

Blastula protease 10 (BP10) is a metalloenzyme involved in sea urchin embryogenesis, which has been assigned to the astacin family of zinc-dependent endopeptidases. It shows greatest homology with the mammalian tolloid-like genes and contains conserved structural motifs consistent with astacin, tolloid, and bone morphogenetic protein 1. Astacin, a crustacean digestive enzyme, has been proposed to carry out hydrolysis via a metal-centered mechanism that involves a metal-coordinated "tyrosine switch." It has not been determined if the more structurally complex members of this family involved in eukaryotic development share this mechanism. The recombinant BP10 has been overexpressed in Escherichia coli, its metalloenzyme nature has been confirmed, and its catalytic properties have been characterized through kinetic studies. BP10 shows significant hydrolysis toward gelatin both in its native zinc-containing form and copper derivative. The copper derivative of BP10 shows a remarkable 960% rate acceleration toward the hydrolysis of the synthetic substrate N-benzoyl-arginine-p-nitroanilide when compared with the zinc form. The enzyme also shows calcium-dependent activation. These are the first thorough mechanistic studies reported on BP10 as a representative of the more structurally complex members of astacin-type enzymes in deuterostomes, which can add supporting data to corroborate the metal-centered mechanism proposed for astacin and the role of the coordinated Tyr. We have demonstrated the first mechanistic study of a tolloid-related metalloenzyme involved in sea urchin embryogenesis.

Animals↗

Making mechanistic connections between cell signaling pathways and pathological endpoints.

Cell signaling is a term used to describe a complex interactive system of signals that act to regulate or mediate a cellular response. Therapies that target cell signaling pathways have the potential to effectively reverse molecular deregulation underlying disease. The inherent complexity of cell signaling presents a major challenge to designing such therapies however, because perturbation of pathways has the potential to produce dramatic adverse effects. Pathologists are in the primary position of detecting adverse responses in drug development and are essential members of teams whose goal is to determine the mechanisms underlying tissue responses. The pathologist therefore will be expected to integrate morphologic interpretation with data obtained from several laboratory-based methods and data derived from novel technologies. Approaches being used include several in silico tools that provide access to public databases and signal pathway visualization that can serve to focus on key mechanistic hypotheses. The main objective of this article is to discuss a basic mechanistic approach and methods that can be used to associate modulation of cell signaling pathways with pathologic endpoints. The approach suggested begins with diagnostic pathology and uses global gene expression analysis in conjunction with transcription factor profiling and confirmatory protein technologies, to elucidate pathways relevant to the biological mechanism. Another important objective is to highlight the use of in silico technologies to prioritize laboratory efforts and focus these efforts on key hypotheses.

Animals↗

Inhalation toxicity of propineb. Part II: Results of mechanistic studies in rats.

Previous repeated inhalation exposure studies revealed two independent organotropic effects of inhaled propineb dust: One was restricted to the lung, the other to muscle weakness of hindlimbs. These effects were believed to be causally related to the principle decomposition products of this type of dithiocarbamate in the biological milieu and related to zinc and carbon disulfide. Two mechanistic 1-wk inhalation studies were performed, each focusing on one of these findings. The 7 x 6-h/day repeated-exposure inhalation study analyzed whether the nature of the response occurring at the alveolar level is "adaptive" or "early adverse" and whether soluble zinc is the causative agent. Groups of 18 female rats were exposed nose-only to mean concentrations of 0, 1.1, 5.5, and 25.8 mg propineb/m(3) and 6.9 mg ZnO/m(3). On postexposure days 1, 3, and 15 the time course of responses was analyzed by bronchoalveolar lavage (BAL), including quantification of Zn and metallothionein (MT) in BAL cells. Clinical evidence of muscular weakness was investigated separately in 20 female Wistar rats exposed to 70 mg propineb/m(3) on 5 consecutive days (6 h/day), followed by a 2-wk postexposure period. Clinical signs, body weights, and feed and water consumption were recorded as frequently as technically feasible. Fifty percent of rats received an oral cysteine supplementation to verify/refute the hypothesis that the incapacitation observed in previous studies is the cause of emaciation and associated impairment of CS(2) detoxification. The findings of the first study are consistent with this hypothesis, namely, that soluble Zn triggers a series of pulmonary events that is consistent with the homeostasis of this essential metal. It is concluded, accordingly, that the adjusted maximal workplace level for ZnO is also valid for propineb to preclude Zn-mediated responses to occur in the lung. With respect to muscular effects, this mechanistic study demonstrates further that the increased detoxification capacity afforded by oral supplementation of cysteine mitigates markedly the toxic potency of propineb. Procedural variables specific to the inhalation bioassay appear to be decisive for the elicitation of muscular effects. The major variable is considered to be the large drop in body weights associated with each exposure session and the concomitantly decreased uptake of essential nutritional factors (e.g., cysteine) involved in the detoxification of this compound. Accordingly, the muscular deficits elicited by high concentrations of propineb are viewed to be secondary effects in an animal species likely to be more susceptible to this type of change than humans (Pauluhn & Rosenbruch, 2003).

Administration, Inhalation↗

Chemically induced renal tubule tumors in the laboratory rat and mouse: review of the NCI/NTP database and categorization of renal carcinogens based on mechanistic information.

The incidence of renal tubule carcinogenesis in male and female rats or mice with 69 chemicals from the 513 bioassays conducted to date by the NCI/NTP has been collated, the chemicals categorized, and the relationship between carcinogenesis and renal tubule hyperplasia and exacerbation of the spontaneous, age-related rodent disease chronic progressive nephropathy (CPN) examined. Where information on mechanism or mode of action exists, the chemicals have been categorized based on their ability to directly or indirectly interact with renal DNA, or on their activity via epigenetic pathways involving either direct or indirect cytotoxicity with regenerative hyperplasia, or exacerbation of CPN. Nine chemicals were identified as directly interacting with DNA, with six of these producing renal tubule tumors at high incidence in rats of both sexes, and in some cases also in mice. Ochratoxin A was the most potent compound in this group, producing a high tumor incidence at very low doses, often with metastasis. Three chemicals were discussed in the context of indirect DNA damage mediated by an oxidative free radical mechanism, one of these being from the NTP database. A third category included four chemicals that had the potential to cause DNA damage following conjugation with glutathione and subsequent enzymatic activation to a reactive species, usually a thiol-containing entity. Two chemicals were allocated into the category involving a direct cytotoxic action on the renal tubule followed by sustained compensatory cell proliferation, while nine were included in a group where the cell loss and sustained increase in renal tubule cell turnover were dependent on lysosomal accumulation of the male rat-specific protein, alpha2mu-globulin. In a sixth category, morphologic evidence on two chemicals indicated that the renal tumors were a consequence of exacerbated CPN. For the remaining chemicals, there were no pertinent data enabling assignment to a mechanistic category. Accordingly, these chemicals, acting through an as yet unknown mechanism, were grouped as either being associated with an enhancement of CPN (category 7, 16 chemicals), or not associated with enhanced CPN (category 8, 4 chemicals). A ninth category dealt with 11 chemicals that were regarded as producing increases in renal tubule tumors that did not reach statistical significance. A 10th category discussed 6 chemicals that induced renal tumors in mice but not in rats, plus 8 chemicals that produced a low incidence of renal tubule tumors in mice that did not reach statistical significance. As more mechanistic data are generated, some chemicals will inevitably be placed in different groups, particularly those from categories 7 and 8. A large number of chemicals in the series exacerbated CPN, but those in category 7 especially may be candidates for inclusion in category 6 when further information is gleaned from the relevant NTP studies. Also, new data on specific chemicals will probably expand category 5 as cytotoxicity and cell regeneration are identified as obligatory steps in renal carcinogenesis in more cases. Additional confirmatory outcomes arising from this review are that metastases from renal tubule tumors, while encountered with chemicals causing DNA damage, are rare with those acting through an epigenetic pathway, with the exception being fumonisin B1; that male rats and mice are generally more susceptible than female rats and mice to chemical induction of renal tubule tumors; and that a background of atypical tubule hyperplasia is a useful indicator reflecting a chemically associated renal tubule tumor response. With respect to renal tubule tumors and human risk assessment, chemicals in categories 1 and 2, and possibly 3, would currently be judged by linear default methods; chemicals in category 4 (and probably some in category 3) as exhibiting a threshold of activity warranting the benchmark approach; and those in categories 5 and 6 as representing mechanisms that have no relevance for extrapolation to humans.

Adenoma↗

The importance of hydrophobicity and electrophilicity descriptors in mechanistically-based QSARs for toxicological endpoints.

Quantitative structure-activity relationship (QSAR) analysis of four toxicological data sets is described. The toxicological data include three data sets retrieved from the literature (the toxic and metabolic effects of 23 aliphatic alcohols on the perfused rat liver; the toxicity of 21 pyridines to mice; the lethality of 55 halogenated hydrocarbons to the mould Aspergillus nidulans). In addition, the toxicity of 13 mono- and di-substituted nitrobenzenes in a 15 min assay using the alga Chlorella vulgaris was analysed. QSARs were developed successfully using descriptors to describe uptake in the organism (i.e. hydrophobicity as quantified by the logarithm of the octanol-water partition coefficient, log P) and reactivity at the site of action (i.e. electrophilicity as quantified by the energy of the lowest unoccupied molecular orbital, E(LUMO)). A further parameter describing molecular branching as also required to model the data for the aliphatic alcohols. The results demonstrate that mechanistically based QSARs can be developed for these diverse endpoints which are, in terms of statistical quality as good as, if not better, than QSARs based on less mechanistically interpretable descriptors.

Animals↗

Movies, measurement, and modeling: the three Ms of mechanistic immunology.

Immunological phenomena that were once deduced from genetic, biochemical, and in situ approaches are now being witnessed in living color, in three dimensions, and in real time. The information in time-lapse imaging can provide valuable mechanistic insight into a host of processes, from cell migration to signal transduction. What we need now are methods to quantitate these new visual data and to exploit computational resources and statistical mechanical methods to develop mechanistic models.

Allergy and Immunology↗

Integrating historical and mechanistic biology enhances the study of adaptation.

Adding a causal, mechanistic dimension to the study of character evolution will increase the strength of inferences regarding the evolutionary history of characters and their adaptive consequences. This approach has the advantage of illuminating mechanism and testing evolutionary hypotheses rigorously. We consider the advantages of combining mechanistic and historical biology in the study of behavior, physiology, and development. We present six examples to illustrate the advantages: (1) preexisting biases in sound perception in frogs; (2) preexisting biases in visual cues in swordtailfishes; (3) exploitation of prey location behavior for attraction of mates in water mites; (4) heterospecific mating in asexual molly fishes; (5) developmental foundation of morphological diversification in amphibian digits; and (6) locomotor performance at low temperature and the evolution of nocturnality in geckos. In each of these examples, the dominant role of history, combined with organismal integration, makes ignoring history a risky proposition.

Adaptation, Physiological↗

Seed dispersal in heterogeneous environments: bridging the gap between mechanistic dispersal and forest dynamics models.

Seed dispersal is an important determinant of vegetation composition. We present a mechanistic model of seed dispersal by wind that incorporates heterogeneous vegetation structure. Vegetation affects wind speeds, a primary determinant of dispersal distance. Existing models combine wind speed and fall velocity of seeds. We expand on them by allowing vegetation, and thus wind profiles, to vary along seed trajectories, making the model applicable to any wind-dispersed plant in any community. Using seed trap data on seeds dispersing from forests into adjacent sites of two distinct vegetation structures, we show that our model was unbiased and accurate, even though dispersal patterns differed greatly between the two structures. Our spatially heterogeneous model performed better than models that assumed homogeneous vegetation for the same system. Its sensitivity to vegetation structure and ability to predict seed arrival when vegetation structure was incorporated demonstrates the model's utility for providing realistic estimates of seed arrival in realistic landscapes. Thus, we begin to bridge mechanistic seed dispersal and forest dynamics models. We discuss the merits of our model for incorporation into forest simulators, applications where such incorporation has been or is likely to be especially fruitful, and future model refinements to increase understanding of seed dispersal by wind.

Acer↗

The overrated role of 'promotion' in mechanistic modelling of radiation carcinogenesis.

It is argued that the 'cellular' dose-response relationships of model parameters cannot be determined from mechanistic model fits to experimental or epidemiologic cancer data. Baseline population cancer incidence data show conclusions about intermediate cell kinetics to be especially questionable. Here we recommend that mechanistic models should be applied solely in one direction: by starting from known cellular dose-response relationships the models aim at providing a biologically motivated consistent description of the development of radiation-induced cancer for different exposures, which is very important for low-dose risk estimation.

Age Factors↗

Linear mechanistic models for the dorsal lateral geniculate nucleus of cat probed using drifting-grating stimuli.

Experiments with sinusoidal visual stimuli in the early visual pathway have traditionally been interpreted in terms of descriptive filter models. We present an alternative mechanistic approach for interpretation of this type of data recorded from X cells in the dorsal lateral geniculate nucleus (dLGN) of cat. A general, linear, rate-based mathematical expression for the geniculate transfer ratio, i.e. the ratio between the first-harmonic components of the output of a geniculate relay cell and its retinal input, is derived. In linear theory this ratio is independent of the signal processing occurring at the retinal level. Further, the ratio is straightforwardly accessible in experiments due to the presence of S-potentials, representing the retinal input, in extracellular recordings from dLGN. The expression accounts for feedforward inputs from retina and intrageniculate interneurons as well as feedback inputs from cortex and the thalamic reticular nucleus and can be used to experimentally test different mechanistic models for the geniculate circuitry. Two examples of this are considered: a purely feedforward model incorporating relay cell inputs from retinal ganglion cells and interneurons, and a model including cortical feedback inhibition of relay cells via intrageniculate interneurons.

Animals↗

A mechanistic-based approach for assessing chemical hazards to parturition.

Evaluations of environmental hazards to pregnancy often overlook the potential for chemicals to disrupt the final event, childbirth. There are relatively few epidemiologic studies on this topic and even fewer toxicologic investigations. Mechanistic-based approaches offset many of the difficulties that are anticipated with intact laboratory animals, such as interspecies variability in the initiating events, and may allow for rapid and relevant assessment of potential chemical hazards. In vitro systems based on knowledge of the cellular events that underlie parturition may, therefore, facilitate investigation of toxicologic aspects of parturition. Nonetheless, limitations of in vitro mechanistic-based approaches exist. Ultimately, the greatest understanding of risk to pregnancy from environmental chemicals is likely to result from the collaborative efforts of laboratory scientists and epidemiologists.

Animals↗

A new approach to evaluate mechanistic relationships among genotoxic phenomena: validation.

In order to determine its applicability for the study of genotoxicity, a recently developed method to probe for possible mechanistic relationships among toxicological phenomena was applied to the induction of mutations in Salmonella typhimurium. Since the basis of this phenomenon is understood, this would provide a test of the applicability of the new method to DNA-based mechanisms. The results presented indicate that significant relationships are indeed found among phenomena involving damage to or modification of DNA but not between them and non-genotoxic phenomena. The present results suggest that the newly developed approach could be applied to test mechanistic hypotheses involving genotoxic phenomena.

Animals↗

Mechanistic studies show that (-)-FTC-TP is a better inhibitor of HIV-1 reverse transcriptase than 3TC-TP.

Of all of the nucleoside inhibitors approved by the FDA for treatment of AIDS, (-)-beta-2',3'-dideoxy-3'-thiacytidine (3TC, lamivudine) is the only one with the unnatural (-)-beta-L configuration. The fluorinated derivative (-)-beta-2', 3'-dideoxy-5-fluoro-3'-thiacytidine [(-)-FTC] and its triphosphate form have also been reported to have excellent antiretroviral activity against HIV-1 reverse transcriptase (RT). Preliminary results of clinical trials suggest that (-)-FTC is 6- to 10-fold more potent than 3TC. However, the molecular mechanism for the observed enhanced clinical potency of (-)-FTC to inhibit viral replication is not understood. The present mechanistic studies used a transient kinetic approach and were designed to compare the incorporation of 3TC-TP and (-)-FTC-TP into DNA by HIV-1 RT and illuminate key features that may play a role in the differential potency. Here we show that (-)-FTC-TP is incorporated 10-fold more efficiently than 3TC-TP during HIV-1 RT-catalyzed RNA-dependent DNA synthesis. The enhanced incorporation efficiency of (-)-FTC-TP may be a key mechanistic feature that, in part, is responsible for the enhanced potency of (-)-FTC observed in ongoing clinical trials.

Base Sequence↗

Retention of inhaled 238PuO2 in beagles: a mechanistic approach to description.

Groups of Beagle dogs received inhalation exposure to one of three sizes of monodisperse or a polydisperse aerosol of 238PuO2. Periodic sacrifice of pairs of dogs through 4 yr after inhalation exposure provided data on the retention, translocation and mode of excretion of 238Pu. Fragmentation of 238PuO2 particles deposited in lung led to enhanced dissolution, translocation and excretion of 238Pu compared to previous studies using 239PuO2. A mechanistic simulation model was formulated to account for particle dissolution and fragmentation. This model provided adequate prediction of the time course of lung retention, uptake and retention in other organs and excretion. Predictions of the model provided more accurate description of the data than the Task Group on Lung Dynamics model incorporated in the ICRP Publication 30. The mechanistic model provided estimates of cumulative radiation dose to liver and bone that are a factor of five greater and to lung that are a factor of two less than predicted by the Task Group Lung Model.

Aerosols↗

Gadobenate dimeglumine 0.5 M solution for injection (MultiHance) as contrast agent for magnetic resonance imaging of the liver: mechanistic studies in animals.

Mechanistic studies regarding the action of gadobenate dimeglumine (Gd-BOPTA/Dimeg; MultiHance) in animals are presented, and the relevance of the results to protocols for MR imaging of the liver are discussed. Gd-BOPTA/Dimeg maintains all the characteristics of an extracellular contrast agent, but owing to a weak affinity for serum albumin, provides in these applications stronger signal intensities than contrast agents without such affinity at the same dose. This property can be taken advantage of for dynamic liver imaging. A unique property of Gd-BOPTA/Dimeg is that the contrast effective ion, Gd-BOPTA2-, enters hepatocytes selectively and reversibly through the sinusoidal plasma membrane using transport mechanisms other than the organic anion transport polypeptide. In a rate-limiting step, the ion is excreted by the multispecific organic anion transporter into the bile. The increase in liver distribution space of Gd-BOPTA2-, as compared to that of purely extracellular contrast agents, is identified as the principal mechanism of normal parenchymal signal enhancement. Microviscosity effects inside hepatocytes add to the relaxation effectiveness of Gd-BOPTA2-, while its presence in the bile and an affinity for intracellular macromolecules play subordinate roles only. Gd-BOPTA2- persists in hepatocytes beyond the times characteristic of dynamic imaging, providing delayed-phase contrast between normal hepatocytes and tumor cells. As a result, the conspicuity of small focal lesions and thus their detection is improved. Additionally, Gd-BOPTA/Dimeg allows sites of abscesses and systemically damaged tissue to be distinguished from healthy liver. Taken together these mechanistically-supported properties qualify the product as a versatile general MR contrast agent with added merits in liver imaging.

Animals↗