α-Amylase from germinating soybean (Glycine max) seeds – Purification,characterization and sequential similarity of conserved and catalytic amino acid residues

Starch hydrolyzing amylase from germinated soybeans seeds (Glycine max) has been purified 400-fold to electrophoretic homogeneity with a final specific activity of 384 units/mg. SDS–PAGE of the final preparation revealed a single protein band of 100 kDa, whereas molecular mass was determined to be 84 kDa by MALDI–TOF and gel filtration on Superdex-200 (FPLC). The enzyme exhibited maximum activity at pH 5.5 and a pI value of 4.85. The energy of activation was determined to be 6.09 kcal/mol in the temperature range 25–85 °C. Apparent Michaelis constant (K_m(app)) for starch was 0.71 mg/mL and turnover number (k_cat) was 280 s^?1 in 50 mM sodium acetate buffer, pH 5.5. Thermal inactivation studies at 85 °C showed first-order kinetics with rate constant (k) equal to 0.0063 min^?1. Soybean α-amylase showed high specificity for its primary substrate starch. High similarity of soybean α-amylase with known amylases suggests that this α-amylase belongs to glycosyl hydrolase family 13. Cereal α-amylases have gained importance due to their compatibility for biotechnological applications. Wide availability and easy purification protocol make soybean as an attractive alternative for plant α-amylase. Soybean can be used as commercially viable source of α-amylase for various industrial applications.     

Large domain fluctuations on 50-ns timescale enable catalytic activity in phosphoglycerate kinase

Large-scale domain motions of enzymes are often essential for their biological function. Phosphoglycerate kinase has a wide open domain structure with a hinge near the active center between the two domains. Applying neutron spin echo spectroscopy and small-angle neutron scattering we have investigated the internal domain dynamics. Structural analysis reveals that the holoprotein in solution seems to be more compact compared to the crystal structure but would not allow the functionally important phosphoryl transfer between the substrates if the protein were static. Brownian large-scale domain fluctuation dynamics on a timescale of 50 ns was revealed by neutron spin echo spectroscopy. The dynamics observed was compared to the displacement patterns of low-frequency normal modes. The displacements along the normal-mode coordinates describe our experimental results reasonably well. In particular, the domain movements facilitate a close encounter of the key residues in the active center to build the active configuration. The observed dynamics shows that the protein has the flexibility to allow fluctuations and displacements that seem to enable the function of the protein. Moreover, the presence of the substrates increases the rigidity, which is deduced from a faster dynamics with smaller amplitude.     

Does elevated atmospheric carbon dioxide affect arbuscular mycorrhizas?

It is well established that an increase in the concentration of atmospheric CO(2) stimulates plant growth. Recently, many researchers have concluded that elevated CO(2) concentrations also stimulate mycorrhizal colonization. However, new evidence suggests that the observed CO(2) effects on arbuscular mycorrhizal fungi are indirect and are a result of faster plant growth at higher CO(2) concentrations. Potential changes to species assemblages of mycorrhizal fungi could affect soil carbon storage and, consequently, the feedback effects of terrestrial soil-vegetation systems on global environmental change.     

Conformational State Distributions and Catalytically Relevant Dynamics of a Hinge-Bending Enzyme Studied by Single-Molecule FRET and a Coarse-Grained Simulation

Over the last few decades, a view has emerged showing that multidomain enzymes are biological machines evolved to harness stochastic kicks of solvent particles into highly directional functional motions. These intrinsic motions are structurally encoded, and Nature makes use of them to catalyze chemical reactions by means of ligand-induced conformational changes and states redistribution. Such mechanisms align reactive groups for efficient chemistry and stabilize conformers most proficient for catalysis. By combining single-molecule Förster resonance energy transfer measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained results for a hinge-bending enzyme, namely phosphoglycerate kinase (PGK), which support and extend these ideas. From single-molecule Förster resonance energy transfer, we obtained insight into the distribution of conformational states and the dynamical properties of the domains. The simulations allowed for the characterization of interdomain motions of a compact state of PGK. The data show that PGK is intrinsically a highly dynamic system sampling a wealth of conformations on timescales ranging from nanoseconds to milliseconds and above. Functional motions encoded in the fold are performed by the PGK domains already in its ligand-free form, and substrate binding is not required to enable them. Compared to other multidomain proteins, these motions are rather fast and presumably not rate-limiting in the enzymatic reaction. Ligand binding slightly readjusts the orientation of the domains and feasibly locks the protein motions along a preferential direction. In addition, the functionally relevant compact state is stabilized by the substrates, and acts as a prestate to reach active conformations by means of Brownian motions.     

Picosecond molecular motions in bacteriorhodopsin from neutron scattering.

The characteristics of internal molecular motions of bacteriorhodopsin in the purple membrane have been studied by quasielastic incoherent neutron scattering. Because of the quasihomogeneous distribution of hydrogen atoms in biological molecules, this technique enables one to study a wide variety of intramolecular motions, especially those occurring in the picosecond to nanosecond time scale. We performed measurements at different energy resolutions with samples at various hydration levels within a temperature range of 10-300 K. The analysis of the data revealed a dynamical transition at temperatures Td between 180 K and 220 K for all motions resolved at time scales ranging from 0.1 to a few hundred picoseconds. Whereas below Td the motions are purely vibrational, they are predominantly diffusive above Td, characterized by an enormously broad distribution of correlation times. The variation of the hydration level, on the other hand, mainly affects motions slower than a few picoseconds.     

Perceptions of Health Communication,Water Treatment and Sanitation in Artibonite Department,Haiti, March-April 2012

The international response to Haiti’s ongoing cholera outbreak has been multifaceted, including health education efforts by community health workers and the distribution of free water treatment products. Artibonite Department was the first region affected by the outbreak. Numerous organizations have been involved in cholera response efforts in Haiti with many focusing on efforts to improve water, sanitation, and hygiene (WASH). Multiple types of water treatment products have been distributed, creating the potential for confusion over correct dosage and water treatment methods. We utilized qualitative methods in Artibonite to determine the population’s response to WASH messages, use and acceptability of water treatment products, and water treatment and sanitation knowledge, attitudes and practices at the household level. We conducted eighteen focus group discussions (FGDs): 17 FGDs were held with community members (nine among females, eight among males); one FGD was held with community health workers. Health messages related to WASH were well-retained, with reported improvements in hand-washing. Community health workers were identified as valued sources of health information. Most participants noted a paucity of water-treatment products. Sanitation, specifically the construction of latrines, was the most commonly identified need. Lack of funds was the primary reason given for not constructing a latrine. The construction and maintenance of potable water and sanitation services is needed to ensure a sustainable change.     

Respiration of the external mycelium in the arbuscular mycorrhizal symbiosis shows strong dependence on recent photosynthates and acclimation to temperature

* Although arbuscular mycorrhizal (AM) fungi are a major pathway in the global carbon cycle, their basic biology and, in particular, their respiratory response to temperature remain obscure. * A pulse label of the stable isotope (13)C was applied to Plantago lanceolata, either uninoculated or inoculated with the AM fungus Glomus mosseae. The extra-radical mycelium (ERM) of the fungus was allowed to grow into a separate hyphal compartment excluding roots. We determined the carbon costs of the ERM and tested for a direct temperature effect on its respiration by measuring total carbon and the (13)C:(12)C ratio of respired CO(2). With a second pulse we tested for acclimation of ERM respiration after 2 wk of soil warming. * Root colonization remained unchanged between the two pulses but warming the hyphal compartment increased ERM length. delta(13)C signals peaked within the first 10 h and were higher in mycorrhizal treatments. The concentration of CO(2) in the gas samples fluctuated diurnally and was highest in the mycorrhizal treatments but was unaffected by temperature. Heating increased ERM respiration only after the first pulse and reduced specific ERM respiration rates after the second pulse; however, both pulses strongly depended on radiation flux. * The results indicate a fast ERM acclimation to temperature, and that light is the key factor controlling carbon allocation to the fungus.     

How aggregation and conformational scrambling of unfolded states govern fluorescence emission spectra

In a case study on five homologous alpha-amylases we analyzed the properties of unfolded states as obtained from treatments with GndHCl and with elevated temperatures. In particular the wavelength of the tryptophan fluorescence emission peak (lambda(max)) is a valuable parameter to characterize properties of the unfolded state. In all cases with a typical red shift of the emission spectrum occurring during structural unfolding we observed a larger magnitude of this shift for GndHCl-induced unfolding as compared to thermal unfolding. Although a quantitative relation between aggregation and reduction of the unfolding induced red shifts cannot be given, our data indicate that protein aggregation contributes significantly to smaller magnitudes of red shifts as observed during thermal unfolding. In addition, other properties of the unfolded states, most probable structural compactness or simply differences in the conformational scrambling, also affect the magnitude of red shifts. For the irreversible unfolding alpha-amylases studied here, transition temperatures and magnitudes of red shifts are strongly depending on heating rates. Lower protein concentrations and smaller heating rates lead to larger red shifts upon thermal unfolding, indicating that under these conditions the protein aggregation is less pronounced.     

Activity and stability of a thermostable alpha-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation

To elucidate how enzymes adapt to extreme environmental conditions, a comparative study with a thermostable alpha-amylase from Bacillus licheniformis (BLA) and its mesophilic homologue from Bacillus amyloliquefaciens (BAA) was performed. We measured conformational stability, catalytic activity, and conformational fluctuations on the picosecond time scale for both enzymes as a function of temperature. The objective of this study is to analyze how these properties are related to each other. BLA shows its maximal catalytic activity at about 90-95 degrees C and a strongly reduced activity (only 20% of the maximum) at room temperature. Although B. licheniformis itself is a mesophilic organism, BLA shows an activity profile typical for a thermophilic enzyme. In contrast to this, BAA exhibits its maximal activity at about 80 degrees C but with a level of about 60% activity at room temperature. In both cases the unfolding temperatures T(m) are only 6 degrees C (BAA, T(m) = 86 degrees C) and 10 degrees C (BLA, T(m) = 103 degrees C), respectively, higher than the temperatures for maximal activity. In contrast to many previous studies on other thermophilic-mesophilic pairs, in this study a higher structural flexibility of the thermostable BLA was measured as compared to the mesophilic BAA. The findings of this study neither indicate a proportionality between the observed dynamics and the catalytic activity nor support the idea of more "rigid" thermostable proteins, as often proposed in the concept of "corresponding states".     

Root production, turnover and respiration under two grassland types along an altitudinal gradient: influence of temperature and solar radiation

 We have measured the rates of root production and death and of root respiration in situ under two grasslands along an altitudinal gradient in the northern Pennines, UK, represented by a lowland site at 171 m in an agricultural setting, and three upland sites between 480 and 845 m. One grassland was dominated by Festuca ovina and was on a brown earth soil; the other was dominated by Juncus squarrosus and Nardus stricta and occurred on a peaty gley. The natural altitudinal gradient was extended by transplantation. Although root biomass and root production (estimated using minirhizotrons) both showed pronounced seasonal peaks, there was no simple altitudinal gradient in either variable, and neither root production nor root death rate was a simple function of altitude. Increased root accumulation in summer was a function of change in the length of the growing season, not of soil temperature. Root populations in winter were similar at all sites, showing that increased production at some sites was accompanied by increased turnover, a conclusion confirmed by cohort analyses. Respiration rate, measured in the field by extracting roots and measuring respiration at field temperature in an incubator, was unrelated to temperature. The temperature sensitivity of respiration (expressed as the slope of a plot of log respiration rate against temperature) showed no simple seasonal or altitudinal pattern. Both root growth (under Festuca) and respiration rate were, however, closely related to radiation fluxes, averaged over the previous 10 days for growth and 2 days for respiration. The temperature sensitivity of respiration was a function of soil temperature at the time of measurement. These results show that root growth and the consequent input of carbon to soil in these communities is controlled by radiation flux not temperature, and that plants growing in these upland environments may acclimate strongly to low temperatures. Most carbon cycle models assume that carbon fluxes to soil are powerfully influenced by temperature, but that assumption is based largely on short-term studies and must be reassessed. Received: 11 August 1997 / Accepted: 25 October 1997