Effects of mutations of active site residues and amino acids interacting with the Ω loop on substrate activation of butyrylcholinesterase

The peripheral anionic site (PAS) of human butyrylcholinesterase is involved in the mechanism of substrate activation by positively charged substrates and ligands. Two substrate binding loci, D70 in the PAS and W82 in the active site, are connected by the Ω loop. To determine whether the Ω loop plays a role in the signal transduction between the PAS and the active site, residues involved in stabilization of the loop, N83, K339 and W430, were mutated. Mutations N83A and N83Q caused loss of substrate activation, suggesting that N83 which interacts with the D70 backbone may be an element of the transducing system. The K339M and W430A mutant enzymes retained substrate activation. Residues W82, E197, and A328 in the active site gorge have been reported to be involved in substrate activation. At butyrylthiocholine concentrations greater then 2 mM, W82A showed apparent substrate activation. Mutations E197Q and E197G strongly reduced substrate activation, while mutation E197D caused a moderate effect, suggesting that the carboxylate of residue E197 is involved in substrate activation. Mutations A328F and A328Y showed no substrate activation, whereas A328G retained substrate activation. Substrate activation can result from an allosteric effect due to binding of the second substrate molecule on the PAS. Mutation W430A was of special interest because this residue hydrogen bonds to W82 and Y332. W430A had strongly reduced affinity for tetramethylammonium. The bimolecular rate constant for reaction with diisopropyl fluorophosphate was reduced 10 000-fold, indicating severe alteration in the binding area in W430A. The k_cat values for butyrylthiocholine, o-nitrophenyl butyrate, and succinyldithiocholine were lower. This suggested that the mutation had caused misfolding of the active site gorge without altering the Ω loop conformation/dynamics. W430 as well as W231 and W82 appear to form the wall of the active site gorge. Mutation of any of these tryptophans disrupts the architecture of the active site.     

Does the proposed DSE motif form the active center in the Hermes transposase?

Donor cleavage and strand transfer are two functions performed by transposases during transposition of class II transposable elements. Within transposable elements, the only active center described, to date, facilitating both functions, is the so-called DDE motif. A second motif, R-K-H/K-R-H/W-Y, is found in the site-specific recombinases of the tyrosine recombinase family. While present in many bacterial insertion sequences as well as in the eukaryotic family of mariner/Tc1 elements, the DDE motif was considered absent in other classes of eukaryotic class II elements such as P, and hAT and piggyBac. Based on sequence alignments of a hobo-like element from the nematode Caenorhabditis elegans, to a variety of other hAT transposases and several members of the mariner/Tc1 group, Bigot et al. [Gene 174 (1996) 265] proposed the presence of a DSE motif in hAT transposases. In the present study we tested if each of these three residues is required for transposition of the Hermes element, a member of the hAT family commonly used for insect transformation. While D402N and E572Q mutations lead to knock-out of Hermes function, mutations S535A and S535D did not affect transposition frequency or the choice of integration sites. These data give the first experimental support that D402 and E572 are indeed required for transposition of Hermes. Furthermore, this study indicates that the active center of the Hermes transposase differs from the proposed DSE motif. It remains to be shown if other residues also form the active site of this transposase.     

Functional analysis of conserved aromatic amino acids in the discoidin domain of Paenibacillus β-1,3-glucanase

The 190-kDa Paenibacillus β-1,3-glucanase (LamA) contains a catalytic module of the glycoside hydrolase family 16 (GH16) and several auxiliary domains. Of these, a discoidin domain (DS domain), present in both eukaryotic and prokaryotic proteins with a wide variety of functions, exists at the carboxyl-terminus. To better understand the bacterial DS domain in terms of its structure and function, this domain alone was expressed in Escherichia coli and characterized. The results indicate that the DS domain binds various polysaccharides and enhances the biological activity of the GH16 module on composite substrates. We also investigated the importance of several conserved aromatic residues in the domain's stability and substrate-binding affinity. Both were affected by mutations of these residues; however, the effect on protein stability was more notable. In particular, the forces contributed by a sandwiched triad (W1688, R1756, and W1729) were critical for the presumable β-sandwich fold.     

Does the anthropometric model influence whole-body center of mass calculations in gait?

Examining whole-body center of mass (COM) motion is one of method being used to quantify dynamic balance and energy during gait. One common method for estimating the COM position is to apply an anthropometric model to a marker set and calculate the weighted sum from known segmental COM positions. Several anthropometric models are available to perform such a calculation. However, to date there has been no study of how the anthropometric model affects whole-body COM calculations during gait. This information is pertinent to researchers because the choice of anthropometric model may influence gait research findings and currently the trend is to consistently use a single model. In this study we analyzed a single stride of gait data from 103 young adult participants. We compared the whole-body COM motion calculated from 4 different anthropometric models (Plagenhoef et al., 1983; Winter, 1990; de Leva, 1996; Pavol et al., 2002). We found that anterior-posterior motion calculations are relatively unaffected by the anthropometric model. However, medial-lateral and vertical motions are significantly affected by the use of different anthropometric models. Our findings suggest that the researcher carefully choose an anthropometric model to fit their study populations when interested in medial-lateral or vertical motions of the COM. Our data can provide researchers a priori information on the model determination depending on the particular variable and how conservative they may want to be with COM comparisons between groups.     

Occurrence of mycosporine-like amino acids in the red-tide dinoflagellate Alexandrium excavatum: UV-photoprotective compounds?

Water extracts of the red-tide dinoflagellate Alexandrium excavatumgrown at ‘high’ light intensity (200 µE m^–2s^–1) show a broad absorbance maximum in the UV regionof the spectrum (310–360 nm). Using TLC and reverse-phaseHPLC a series of mycosporine-like amino acids have been characterized:mycosporine-glycine (_max = 310 nm), palythine (_max = 320 nm),asterina-330 (_max = 330 nm), shinorine (_max = 334 nm), porphyra-334(_max= 334 nm), palythenic acid (_max = 337 nm) and the isomericmixture of usujirene and palythene (_max = 359 nm). From theobserved spectral changes during transference from ‘low’(20 µE m^–2 s^–1) to ‘high’ (200µE m^–2 s^–1) light intensities and vice versa,the series of compounds are supposed to be biogenically relatedto one another. The presence of these compounds in A.excavatumis discussed in relation to their possible role in the photoprotectionto deleterious UV radiation.     

Does water play a structural role in the folding of small nucleic acids?

Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5'-GGGC[GCAA]GCCU-3') via ensemble molecular dynamics simulation and, with nearly 500 micros of aggregate simulation time using an explicit representation of the ionic solvent, report successful ensemble folding simulations with a predicted folding time of 8.8(+/-2.0) micros, in agreement with experimental measurements of approximately 10 micros. Comparing our results to previous folding simulations using the GB/SA continuum solvent model shows that accounting for water-mediated interactions is necessary to accurately characterize the free energy surface and stochastic nature of folding. The formation of the secondary structure appears to be more rapid than the fastest ionic degrees of freedom, and counterions do not participate discretely in observed folding events. We find that hydrophobic collapse follows a predominantly expulsive mechanism in which a diffusion-search of early structural compaction is followed by the final formation of native structure that occurs in tandem with solvent evacuation.     

Molecular orbital calculation for the model compounds of kainoid amino acids, agonists of excitatory amino acid receptors. Does the kainoid C4-substituent directly interact with the receptors?

Kainoid amino acids are agonists of the AMPA/kainate receptors and exhibit highly potent neuroexcitatory activity. From the results of extensive structure--activity relationship studies, we previously postulated that the C4-substituent of the kainoid amino acids interacts with an allosteric site of the glutamate receptor with electron-donating character. In order to investigate the mode of action in more detail, molecular orbital calculation for model compounds of the kainoid were performed. The results indicated that the HOMO energy level of the C4-substituent is involved in the potent neuroexcitatory activity, thus supporting our hypothesis.     

Does an increase in reward affect the precision of the encoding of directional information in the honeybee waggle dance?

Apis mellifera foragers perform waggle dances to communicate the presence of highly desirable nectar sources to their forager-mates. Each waggle dance consists of several waggle-runs (straight movements of the dancer closely aligned on the comb surface) that carry spatial information that the dance followers can use to locate the food source being advertised. To address how this complex motor display responds to unpredictable fluctuations in its main triggering stimulus, i.e., sucrose stimulation, we analyzed the effects of an increase in reward on the direction of consecutive waggle-runs as well as other components of the waggle dance. Results show that a sudden increase in reward may increase the directional scatter among consecutive waggle-runs, especially those performed at the beginning of the dance. However, a simultaneous and rapid increase in the duration of the signal—together with a more regular alignment of the later waggle-runs within the signal— seems to compensate the initial increase in directional scatter so that the transfer of directional information remains effective. These results point out that the regulation of dance maneuvers depends on the dancers motivation to forage.     

Contribution of an aspartate residue,D114, in the active site of clostridial glutamate dehydrogenase to the enzyme’s unusual pH dependence

Glutamate dehydrogenase from Clostridium symbiosum displays unusual kinetic behaviour at high pH when compared with other members of this enzyme family. Structural and sequence comparisons with GDHs from other organisms have indicated that the Asp residue at position 114 in the clostridial enzyme may account for these differences. By replacing this residue by Asn, a mutant protein has been created with altered functional properties at high pH. This mutant protein can be efficiently overexpressed in Escherichia coli, and several criteria, including mobility in non-denaturing electrophoresis, circular dichroism (CD) spectra and initial crystallisation studies, suggest a folding and an assembly comparable to those of the wild-type protein. The D114N mutant enzyme shows a higher optimum pH for activity than the wild-type enzyme, and both CD data and activity measurements show that the distinctive time-dependent reversible conformational inactivation seen at high pH in the wild-type enzyme is abolished in the mutant.     

Does the Production of an Airbag Injure more People than the Airbag Saves in Traffic?

Social life cycle assessment (S‐LCA) has been discussed for some years in the LCA community. We raise two points of criticism against current S‐LCA approaches. First, the development of S‐LCA methodology has not, to date, been based on experience with actual case studies. Second, for social impacts to be meaningfully assessed in a life cycle perspective, social indicators need to be unambiguously interpreted in all social contexts along the life cycle. We here discuss an empirically based approach to S‐LCA, illustrated by a case study of an automobile airbag system. The aim of the case study is to compare the injuries and lives lost during the product life cycle of the airbag system (excluding waste handling impacts) with the injuries prevented and lives saved during its use. The indicator used for assessing social impacts in this study is disability‐adjusted life years (DALY). The results from this study indicate that the purpose of an airbag system, which is to save lives and prevent injuries, is justified also in a life cycle perspective.     

Does the proportion of arthropods versus fruit in the diet influence overwintering condition of an omnivorous songbird?

Many migratory songbirds switch from a primarily insectivorous diet during the breeding season to either a mixed diet or fruit diet during the non‐breeding season. However, for species with mixed diets, arthropods may be superior food items because of their higher protein content and easier digestibility. We tested this hypothesis by analyzing the diet and body condition of omnivorous Wood Thrushes (Hylocichla mustelina) at a non‐breeding site in tropical forest in Belize, Central America. We used analysis of stable isotopes δ¹⁵N and δ¹³C in the blood to measure diet. Our objective was to determine if a higher dietary proportion of arthropods relative to fruit (i.e., higher δ¹⁵N and δ¹³C) was associated with better body condition. We also examined the possible effect of age, sex, and habitat type on Wood Thrush diets, as well as any changes in diet through the overwintering period. We used a hierarchical Bayesian mixing model (MixSIAR) to estimate the proportion of different prey items in the diet of overwintering Wood Thrushes overall, in each habitat type, and over time during the non‐breeding period. From January to April, we found a significant decline in δ¹⁵N in forest habitats, whereas δ¹⁵N increased in scrub habitat. There was no significant seasonal change in δ¹³C. Birds with higher δ¹⁵N or δ¹³C values were not in better body condition. Females in dry‐scrub habitat consumed more fruit than males, but this did not affect body condition. Mixing model results indicated that most Wood Thrushes at our study sites consumed primarily arthropods, even during the driest times of the non‐breeding season and in the driest habitat. Overall, our results suggest that the diet of Wood Thrushes varies with habitat and during the overwintering period, but diet alone was not a predictor of body condition. Wood Thrushes, and possibly other omnivorous migratory songbirds, are apparently flexibly able to meet their wintering and pre‐migration nutritional demands with a variety of diets.     

Are phloem amino acids involved in the shoot to root control of NO3- uptake in Ricinus communis plants?

The putative role of phloem amino acids as negative feedback signals for root NO3^- uptake was investigated in Ricinus communis L. The NO3^--grown plants were subjected to N-deficiency due either to complete N-deprivation, or to localized N-deprivation on one side of a split-root system. In comparison with controls, complete N-deprivation resulted in a transient increase in ¹⁵NO3^- influx, and in profound changes in downward phloem transport of amino acids. Total amino acid concentration in the phloem sap decreased by 40%, but responses markedly differed between the individual amino acids. Concentrations of Gln and Ser were rapidly lowered by 50%, while those of Val, Phe, Leu, and Ile displayed a marked increase. Localized N-deprivation on one side of the split root system also resulted in the up-regulation of ¹⁵NO3^- influx in the roots still supplied with NO3^-. However, the amino acid composition of the phloem sap directed to these roots was not modified by the treatment, and remained similar to that in N-sufficient control plants. Only amino acid transport to the N-deprived roots was affected as observed in response to complete N-deprivation. The results from split-root plants indicate that the response of root NO3^- influx to N-deficiency is controlled by shoot-borne regulatory signals, and provide a case study where these signals are not related to a qualitative change or a significant decrease in downward phloem transport of amino acids.     

Does fish represent an intermediate stage in the evolution of ureotelic cytosolic arginase I?

Arginase catalyses the last step of the urea cycle. At least two isoenzymes of arginase are known; cytosolic ARG I and mitochondrial ARG II. ARG I is predominantly expressed in liver cytosol, as a part of urea cycle in ureotelic animals. The second isoform ARG II is primarily responsible for non-ureogenic functions, expressed in mitochondria of both hepatic and non-hepatic tissues in most vertebrates. Most micro-organisms and invertebrates are known to have only one type of arginase, whose function is unrelated to ornithine-urea cycle (OUC). However, in ureo-osmotic marine elasmobranchs arginase is localized in liver mitochondria as a part of OUC to synthesize urea for osmoregulation. An evolutionary transition occurred in arginase enzyme in terrestrial ureotelic vertebrates, with the evolution of ARG I from a pre-existing ancestral mitochondrial ARG II. This cytosolic ARG I activity is supposed to have first appeared in lung fishes, but the 40% and 60% distribution of arginase I and II activity in liver and kidney tissue of Heteropneustes fossilis indicates reconsideration of the above fact.     

A genetic approach to the identification of functional amino acids in protein p6 of Bacillus subtilis phage ?29

Protein p6 of the Bacillus subtilis phage ø29 is essential for in vivo viral DNA replication. This protein activates the initiation of ø29 DNA replication in vitro by forming a multimeric nucleoprotein complex at the replication origins. The N-terminal region of protein p6 is involved in DNA binding, as shown by in vitro studies with p6 proteins altered by deletions or missense mutations. We report on the development of an in vivo functional assay for protein p6. This assay is based on the ability of protein p6-producing B. subtilis non-suppressor (su ^–) cells to support growth of a ø29 sus6 mutant phage. We have used this trans-complementation assay to investigate the effect on in vivo viral DNA synthesis of missense mutations introduced into the protein p6 N-terminal region. The alteration of lysine to alanine at position 2 resulted in a partially functional protein, whereas the replacement of arginine by alanine at position 6 gave rise to an inactive protein. These results indicate that arginine at position 6 is critical for the in vivo activity of protein p6. Our complementation system provides a useful genetic approach for the identification of functionally important amino acids in protein p6.     

Does constructive neutral evolution play an important role in the origin of cellular complexity?

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes.     

Does an increase in membrane unsaturated fatty acids account for Tween 80 stimulation of glucosyltransferase secretion by Streptococcus salivarius?

When Streptococcus salivarius was grown in batch culture in the presence of various Tween detergents, the fatty acid moiety of the detergent was incorporated into the lipids of its membrane. Tween 80 (containing primarily oleic acid) markedly stimulated the production of extracellular glucosyltransferase and also increased the degree of unsaturation of the membrane lipid fatty acids. The possibility that an increase in membrane unsaturated fatty acids promoted extracellular glucosyltransferase production was examined by growing cells at different temperatures in the presence or absence of Tween 80. The membrane lipids of cells grown at 30 degrees C, 37 degrees C and 40 degrees C without Tween 80 exhibited unsaturated/saturated fatty acid ratios of 2.06, 1.01 and 0.87 respectively. A significant increase in the production of extracellular glucosyltransferase was observed at 30 degrees C compared to cells grown at 40 degrees C. However, cells produced much more exoenzyme at all temperatures when grown with Tween 80. The results indicated that an increase in the unsaturated fatty acid content of the membrane lipids was not by itself sufficient to account for the stimulation of extracellular glucosyltransferase production by Tween 80, but that the surfactant also had to be present.     

Energy dissipation in photosynthesis: Does the quenching of chlorophyll fluorescence originate from antenna complexes of photosystem II or from the reaction center?

Dissipation of light energy was studied in the moss Rhytidiadelphus squarrosus (Hedw.) Warnst., and in leaves of Spinacia oleracea L. and Arabidopsis thaliana (L.) Heynh., using chlorophyll fluorescence as an indicator reaction. Maximum chlorophyll fluorescence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU)-treated spinach leaves, as produced by saturating light and studied between +5 and −20 °C, revealed an activation energy ΔE of 0.11 eV. As this suggested recombination fluorescence produced by charge recombination between the oxidized primary donor of photosystem II and reduced pheophytin, a mathematical model explaining fluorescence, and based in part on known characteristics of primary electron-transport reactions, was developed. The model permitted analysis of different modes of fluorescence quenching, two localized in the reaction center of photosystem II and one in the light-harvesting system of the antenna complexes. It predicted differences in the relationship between quenching of variable fluorescence F _v and quenching of basal, so-called F ₀ fluorescence depending on whether quenching originated from antenna complexes or from reaction centers. Such differences were found experimentally, suggesting antenna quenching as the predominant mechanism of dissipation of light energy in the moss Rhytidiadelphus, whereas reaction-center quenching appeared to be important in spinach and Arabidopsis. Both reaction-center and antenna quenching required activation by thylakoid protonation but only antenna quenching depended on or was strongly enhanced by zeaxanthin. De-protonation permitted relaxation of this quenching with half-times below 1 min. More slowly reversible quenching, tentatively identified as so-called q _I or photoinhibitory quenching, required protonation but persisted for prolonged times after de-protonation. It appeared to originate in reaction centers. Received: 8 April 2000 / Accepted: 31 August 2000