An ab-initio study of the proton affinity of conjugated schiff-base and related nitrogen compounds: an analysis of the triggering site of bacteriorhodopsin

The chemical groups which take part in the proton transfer reaction in bacteriorhodopsin have been studied by ab initio quantum chemical methods. The various factors such as conjugation with a linear system, electron delocalization of the guanidine type, cis-trans isomerism, geometry distortion and hydrogen bonding with charged groups can influence the properties of a given chemical group. Several systems are studied at 4-31G and STO-3G levels. Some of the Schiff-base analogues and guanidine type molecules are characterized by their molecular orbital diagrams, energy levels and the nature of charge distribution. Also, the effects of the above-mentioned factors on proton affinity are studied. It is hoped that the values thus obtained can be helpful in evaluating various structural models for proton transfer.

Natural Convection on a Horizontal Cone in a Porous Medium with Non-Uniform Wall Temperature/Concentration or Heat/Mass Flux and Suction/Injection

The steady natural convection flow on a horizontal cone embedded in a saturated porous medium with non-uniform wall temperature/concentration or heat/mass flux and suction/injection has been investigated. Non-similar solutions have been obtained. The nonlinear couple differential equations under boundary layer approximations governing the flow have been numerically solved. The Nusselt and Sherwood numbers are found to depend on the buoyancy forces, suction/injection rates, variation of wall temperature/concentration or heat/mass flux, Lewis number and the non-Darcy parameter.

Studies on follicular growth in the immature rat and hamster: Effect of a single injection of gonadotropin or estrogen on the rate of3H-thymidine incorporation into ovarian DNAin vitro

Initiation of follicular growth by specific hormonal stimuli in ovaries of immature rats and hamsters was studied by determining the rate of incorporation of3H-thymidine into ovarian DNAin vitro. Incorporation was considered as an index of DNA synthesis and cell multiplication. A single injection of pregnant mare serum gonadotropin could thus maximally stimulate by 18 hr3H-thymidine incorporation into DNA of the ovary of immature hamsters. Neutralization of pregnant mare serum gonadotropin by an antiserum to ovine follicle stimulating hormone only during the initial 8–10 hr and not later could inhibit the increase in3H-thymidine incorporationin vitro observed at 18 hr, suggesting that the continued presence of gonadotropin stimulus was not necessary for this response. The other indices of follicular growth monitored such as ovarian weight, serum estradiol and uterine weight showed discernible increase at periods only after the above initial event. A single injection of estrogen (diethyl stilbesterol or estradiol-l7β) could similarly cause 18 hr later, a stimulation in the rate of incorporation of3H-thymidine into DNAin vitro in ovaries of immature rats. The presence of endogenous gonadotropins, however, was obligatory for observing this response to estrogen. Evidence in support of the above was two-fold: (i) administration of antiserum to follicle stimulating hormone or luteinizing hormone along with estrogen completely inhibited the increase in3H-thymidine incorporation into ovarian DNAin vitro; (ii) a radioimmunological measurement revealed following estrogen treatment, the presence of a higher concentration of endogenous follicle stimulating hormone in the ovary. Finally, administration of varying doses of ovine follicle stimulating hormone along with a constant dose of estrogen to immature rats produced a dose-dependent increment in the incorporation of3H-thymidine into ovarian DNAin vitro. These observations suggested the potentiality of this system for developing a sensitive bioassay for follicle stimulating hormone.

Site of synthesis of cytochrome P-450 in liver

The suggestion that a rapidly sedimenting rough endoplasmic reticulum fraction in close association with mitochondria, is the preferred site of cytochrome P-450 synthesis has been examined. The rate of cytochrome P-450 synthesis in the different subcellular fractions has been evaluated Image , using the immunoprecipitation technique. The results indicate that the conventional microsomal fraction (100,000 X g sediment) is the major site of cytochrome P-450 synthesis and that the rapidly sedimenting rough endoplasmic reticulum fraction associated with mitochondria is not a preferred site for the hemoprotein synthesis.

Studies on active site mutants of P-falciparum adenylosuccinate synthetase: Insights into enzyme catalysis and activation

Adenylosuccinate synthetase catalyzes a reversible reaction utilizing IMP, GTP and aspartate in the presence of Mg2+ to form adenylosuccinate, GDP and inorganic phosphate. Comparison of similarly liganded complexes of Plasmodium falciparum, mouse and Escherichia coil AdSS reveals H-bonding interactions involving nonconserved catalytic loop residues (Asn429, Lys62 and Thr307) that are unique to the parasite enzyme. Site-directed mutagenesis has been used to examine the role of these interactions in catalysis and structural organization of P. falciparum adenylosuccinate synthetase (PfAdSS). Mutation of Asn429 to Val, Lys62 to Leu and Thr307 to Val resulted in an increase in K-m values for IMP, GTP and aspartate, respectively along with a 5 fold drop in the k(cat) value for N429V mutant suggesting the role of these residues in ligand binding and/or catalysis. We have earlier shown that the glycolytic intermediate, fructose 1,6 bisphosphate, which is an inhibitor of mammalian AdSS is an activator of the parasite enzyme. Enzyme kinetics along with molecular docking suggests a mechanism for activation wherein F16BP seems to be binding to the Asp loop and inducing a conformation that facilitates aspartate binding to the enzyme active site. Like in other AdSS, a conserved arginine residue (Arg155) is involved in dimer crosstalk and interacts with IMP in the active site of the symmetry related subunit of PfAdSS. We also report on the iochemical characterization of the arginine mutants (R155L, R155K and R155A) which suggests that unlike in E. coil AdSS, Arg155 in PfAdSS influences both ligand binding and catalysis. (C) 2010 Elsevier B.V. All rights reserved.

Studies on Stone Age Housepits in Fennoscandia (4000 - 2000 cal BC) : Changes in ground plan, site location and degree of sedentism

Housepits have a remarkably short research history as compared to Fennoscandian archaeological research on the Stone Age in general. The current understanding of the numbers and the distribution of Stone Age housepits in the Nordic countries has, for the most part, been shaped by archaeological studies carried out over the last twenty to thirty years. The main subjects of this research are Neolithic housepits, which are archaeological remains of semi-subterranean pithouses. This dissertation consists of five peer-reviewed articles and a synthesis paper. The articles deal with the development of housepits as seen in the data gathered from Finland (the Lake Saimaa area and south-eastern Finland) and Russia (the Karelian Isthmus). This synthesis expands the discussion of the changes observed in the Papers to include Fennoscandian housepit research as a whole. Certain changes in the size, shape, environmental location, and clustering of housepits extended into various cultures and ecological zones in northern Fennoscandia. Previously, the evolution of housepits has been interpreted to have been caused by the adaptation of Neolithic societies to prevailing environmental circumstances or to re-organization following contacts with the agrarian Corded Ware/Battle Axe Cultures spreading to North. This dissertation argues for two waves of change in the pithouse building tradition. Both waves brought with them certain changes in the pithouses themselves and in the practices of locating the dwellings in the environment/landscape. The changes in housepits do not go hand in hand with other changes in material culture, nor are the changes restricted to certain ecological environments. Based on current information, it appears that the changes relate primarily to the spread of new concepts of housing and possibly to new technology, as opposed to representing merely a local response to environmental factors. This development commenced already before the birth of the Corded Ware/Battle Axe Cultures. Therefore, the changes are argued to have resulted from the spreading of new ideas through the same networks that actively distributed commodities, exotic goods, and raw materials over vast areas between the southern Baltic Sea, the north-west Russian forest zone, and Fennoscandia.

Understorey vegetation as an indicator of forest site potential in Southern Finland.

The relationship between site characteristics and understorey vegetation composition was analysed with quantitative methods, especially from the viewpoint of site quality estimation. Theoretical models were applied to an empirical data set collected from the upland forests of southern Finland comprising 104 sites dominated by Scots pine (Pinus sylvestris L.), and 165 sites dominated by Norway spruce (Picea abies (L.) Karsten). Site index H100 was used as an independent measure of site quality. A new model for the estimation of site quality at sites with a known understorey vegetation composition was introduced. It is based on the application of Bayes' theorem to the density function of site quality within the study area combined with the species-specific presence-absence response curves. The resulting posterior probability density function may be used for calculating an estimate for the site variable. Using this method, a jackknife estimate of site index H100 was calculated separately for pine- and spruce-dominated sites. The results indicated that the cross-validation root mean squared error (RMSEcv) of the estimates improved from 2.98 m down to 2.34 m relative to the "null" model (standard deviation of the sample distribution) in pine-dominated forests. In spruce-dominated forests RMSEcv decreased from 3.94 m down to 3.16 m. In order to assess these results, four other estimation methods based on understorey vegetation composition were applied to the same data set. The results showed that none of the methods was clearly superior to the others. In pine-dominated forests, RMSEcv varied between 2.34 and 2.47 m, and the corresponding range for spruce-dominated forests was from 3.13 to 3.57 m.

Analysis of performance of a hot gas injection thrust vector control system

The complex three-dimensional flowfield produced by secondary injection of hot gases in a rocket nozzle for thrust vector control is analyzed by solving unsteady three-dimensional Euler equations with appropriate boundary conditions. Various system performance parameters like secondary jet amplification factor and axial thrust augmentation are deduced by integrating the nozzle wall pressure distributions obtained as part of the flowfield solution and compared with measurements taken in actual static tests. The agreement is good within the practical range of secondary injectant flow rates for thrust vector control applications.

Interactions of methoxyamine with pyridoxal-5'-phosphate-Schiff's base at the active site of sheep liver serine hydroxymethyltransferase

The mechanism of interaction of methoxyamine with sheep liver serine hydroxymethyltransferase (EC 2.1.2.1) (SHMT) was established by measuring changes in enzyme activity, visible absorption spectra, circular dichroism and fluorescence, and by evaluating the rate constant by stopped-flow spectrophotometry. Methoxyamine can be considered as the smallest substituted aminooxy derivative of hydroxylamine. It was a reversible noncompetitive inhibitor (Ki = 25 microM) of SHMT similar to O-amino-D-serine. Like in the interaction of O-amino-D-serine and aminooxyacetic acid, the first step in the reaction was very fast. This was evident by the rapid disappearance of the enzyme-Schiff base absorbance at 425 nm with a rate constant of 1.3 x 10(3) M-1 sec-1 and CD intensity at 430 nm. Concomitantly, there was an increase in absorbance at 388 nm (intermediate I). The next step in the reaction was the unimolecular conversion (1.1 x 10(-3) sec-1) of this intermediate to the final oxime absorbing at 325 nm. The identity of the oxime was established by its characteristic fluorescence emission at 460 nm when excited at 360 nm and by high performance liquid chromatography. These results highlight the specificity in interactions of aminooxy compounds with sheep liver serine hydroxymethyltransferase and that the carboxyl group of the inhibitors enhances the rate of the initial interaction with the enzyme.

Source and target enzyme signature in serine protease inhibitor active site sequences

Amino acid sequences of proteinaceous proteinase inhibitors have been extensively analysed for deriving information regarding the molecular evolution and functional relationship of these proteins. These sequences have been grouped into several well defined families. It was found that the phylogeny constructed with the sequences corresponding to the exposed loop responsible for inhibition has several branches that resemble those obtained from comparisons using the entire sequence. The major branches of the unrooted tree corresponded to the families to which the inhibitors belonged. Further branching is related to the enzyme specificity of the inhibitor. Examination of the active site loop sequences of trypsin inhibitors revealed that there are strong preferences for specific amino acids at different positions of the loop. These preferences are inhibitor class specific. Inhibitors active against more than one enzyme occur within a class and confirm to class specific sequence in their loops. Hence, only a few positions in the loop seem to determine the specificity. The ability to inhibit the same enzyme by inhibitors that belong to different classes appears to be a result of convergent evolution

Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.

Sensitivity of wetland methane emissions to model assumptions: application and model testing against site observations

Abstract. Methane emissions from natural wetlands and rice paddies constitute a large proportion of atmospheric methane, but the magnitude and year-to-year variation of these methane sources is still unpredictable. Here we describe and evaluate the integration of a methane biogeochemical model (CLM4Me; Riley et al., 2011) into the Community Land Model 4.0 (CLM4CN) in order to better explain spatial and temporal variations in methane emissions. We test new functions for soil pH and redox potential that impact microbial methane production in soils. We also constrain aerenchyma in plants in always-inundated areas in order to better represent wetland vegetation. Satellite inundated fraction is explicitly prescribed in the model because there are large differences between simulated fractional inundation and satellite observations. A rice paddy module is also incorporated into the model, where the fraction of land used for rice production is explicitly prescribed. The model is evaluated at the site level with vegetation cover and water table prescribed from measurements. Explicit site level evaluations of simulated methane emissions are quite different than evaluating the grid cell averaged emissions against available measurements. Using a baseline set of parameter values, our model-estimated average global wetland emissions for the period 1993–2004 were 256 Tg CH4 yr−1, and rice paddy emissions in the year 2000 were 42 Tg CH4 yr−1. Tropical wetlands contributed 201 Tg CH4 yr−1, or 78 % of the global wetland flux. Northern latitude (>50 N) systems contributed 12 Tg CH4 yr−1. We expect this latter number may be an underestimate due to the low high-latitude inundated area captured by satellites and unrealistically low high-latitude productivity and soil carbon predicted by CLM4. Sensitivity analysis showed a large range (150–346 Tg CH4 yr−1) in predicted global methane emissions. The large range was sensitive to: (1) the amount of methane transported through aerenchyma, (2) soil pH (± 100 Tg CH4 yr−1), and (3) redox inhibition (± 45 Tg CH4 yr−1).