Structure and fluctuation of a Streptomyces subtilisin inhibitor.

The kinetics of the hydrogen-deuterium exchange reaction in a subtilisin inhibitor from Streptomyces albogriseolus has been examined by infrared absorption measurement in aqueous solutions at various pH values and temperatures. In the analysis of each piece of kinetic data, it was assumed that the total 104 peptide hydrogen atoms are classified into three kinetic classes A, B1, and B2, and that the sizes of these classes are 72, 15, and 17, respectively at every pH and at every temperature examined. On the basis of the peak position determined for the amide II band in each stage of the exchange reaction, an approximate assignment was suggested of the A, B1 and B2 respectively to an unordered structure, a beta-structure,and an alpha-helical structure in the molecule. This assignment was supported by infrared absorption measurement of a film of this protein and by circular dichroic study of the solutions. On the basis of the temperature effect on the hydrogen-exchange rate constants and on the basis of ultraviolet absorption study in the higher temperature region (40 to 90 degrees C), a discussion has been made on the nature of the fluctuation of the molecular structure of this protein.     

Structure and atomic fluctuation patterns of potato carboxypeptidase a inhibitor protein

Molecular dynamics (MD) simulation methods were applied to the study of the structural and dynamic fluctuation properties of the potato carboxypeptidase A inhibitor protein (PCI) immersed in a bath of 1259 water molecules. A trajectory of 200 ps was generated at constant temperature and pressure. The crystallographic structure of PCI, as found in its complex with bovine carboxy-peptidase A (CPA), was used to seed the MD simulation. Analyses show that the structure of the PCI core is fairly rigid and stable in itself, and that little deformation is caused by the protein-protein interactions found in the PCI-CPA complex. The N-terminal tail fluctuates to approach the core structure and appears as a relatively disordered region. In contrast, the conformations of the C-terminal tail, which is involved in the inhibitory mechanism, fluctuates in the neighborhood of the X-ray structure in orientations which facilitate CPA binding. Comparison with the structural entries for PCI in water obtained from both 2D-NMR experiments and X-ray data shows that important features of the MD structural results fluctuates between the initial crystal values and those obtained from the NMR solution structure. This fluctuation is not uniform; minor regions move away from the X-ray conformation while they do not approach the NMR conformation. The results reported suggest that the trajectory is long enough to show a behavior that is consistent with the conformational space available to the protein in solution.Abbreviations CPA Carboxypeptidase - DG Distance Geometry - NMR Nuclear Magnetic Resonance - NIS Non Inertial Solvent - MD Molecular Dynamics - PBC Periodic Boundary Conditions - PCI Potato Carboxypeptidase Inhibitor - RMSD Root Mean Square Deviation - a.m.u. Atomic mass unitsCorrespondence to: O. Tapia     

Structure,fluctuation and magnitude of a natural grassland soil metagenome

The soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. Soil has more unknown biodiversity than any other ecosystem. We have applied diverse DNA extraction methods coupled with high throughput pyrosequencing to explore 4.88 × 10⁹ bp of metagenomic sequence data from the longest continually studied soil environment (Park Grass experiment at Rothamsted Research in the UK). Results emphasize important DNA extraction biases and unexpectedly low seasonal and vertical soil metagenomic functional class variations. Clustering-based subsystems and carbohydrate metabolism had the largest quantity of annotated reads assigned although <50% of reads were assigned at an E value cutoff of 10⁻⁵. In addition, with the more detailed subsystems, cAMP signaling in bacteria (3.24±0.27% of the annotated reads) and the Ton and Tol transport systems (1.69±0.11%) were relatively highly represented. The most highly represented genome from the database was that for a Bradyrhizobium species. The metagenomic variance created by integrating natural and methodological fluctuations represents a global picture of the Rothamsted soil metagenome that can be used for specific questions and future inter-environmental metagenomic comparisons. However, only 1% of annotated sequences correspond to already sequenced genomes at 96% similarity and E values of <10⁻⁵, thus, considerable genomic reconstructions efforts still have to be performed.     

Field fluctuation in ionic solutions and its biological significance

The thermal fluctuation of the electric potential, the electric field and the charge density of various modes are theoretically analysed in a homogeneous solution of simple electrolytes. The mean square of the fluctuating potential difference between two points at a finite distance averaged in a finite time and the mean square of the fluctuating field at a point averaged in a finite time are calculated. The response of a macromolecule in the solution to such a time-space averaged potential or field is discussed. Numerical estimation shows that the fluctuating potential or field may be actually important in various biological systems. Connection of the present result with the macroscopic case is also shown.     

蕉园蜘蛛种类及其数量消长调查

初步调查香蕉园的蜘蛛约有20多种,是香蕉害虫的重要天敌,主要栖息于香蕉植株的上部和基部,中部则较少。狼蛛类、蚁蛛、蝇虎、沟瘤蛛等数量较多,常年均可见,而其余种类则在某些月份发生。与水稻田蜘蛛比较,发现蕉园中大多数蜘蛛种类与稻田的相似,仅少数种类是稻田中未有的。     

Kinetic and structural characterization of adsorption-induced unfolding of bovine alpha -lactalbumin.

Conformational changes of bovine alpha-lactalbumin induced by adsorption on a hydrophobic interface are studied by fluorescence and circular dichroism spectroscopy. Adsorption of bovine alpha-lactalbumin on hydrophobic polystyrene nanospheres induces a non-native state of the protein, which is characterized by preserved secondary structure, lost tertiary structure, and release of calcium. This partially denatured state therefore resembles a molten globule state, which is an intermediate in the folding of bovine alpha-lactalbumin. Stopped-flow fluorescence spectroscopy reveals two kinetic phases during adsorption with rate constants k(1) approximately 50 s(-1) and k(2) approximately 8 s(-1). The rate of partial unfolding is remarkably fast and even faster than unfolding induced by the addition of 5.4 m guanidinium hydrochloride to native alpha-lactalbumin. The large unfolding rates exclude the possibility that unfolding of bovine alpha-lactalbumin to the intermediate state occurs before adsorption takes place. Stopped-flow fluorescence anisotropy experiments show that adsorption of bovine alpha-lactalbumin on polystyrene nanospheres occurs within the dead time (15 ms) of the experiment. This shows that the kinetic processes as determined by stopped-flow fluorescence spectroscopy are not affected by diffusion or association processes but are solely caused by unfolding of bovine alpha-lactalbumin induced by adsorption on the polystyrene surface. A scheme is presented that incorporates the results obtained and describes the adsorption of bovine alpha-lactalbumin.     

Adrenaline in various organs of the rat: its origin, location and diurnal fluctuation

In order to examine the origin and location of adrenaline in peripheral organs of mammals, adrenaline and noradrenaline were measured in several organs of the rat after adrenalectomy, guanethidine treatment and imipramine injection. One week after bilateral adrenalectomy, adrenaline disappeared almost completely from the heart, spleen and submaxillary gland. Chronic administration of guanethidine caused decreases in both noradrenaline and adrenaline in the peripheral organs. Injection of imipramine induced a reduction of adrenaline concentration in the spleen and submaxillary gland. It is considered that adrenaline in the peripheral organs of mammals is mostly derived from the adrenal gland and that circulating adrenaline is taken up by sympathetic nerve endings in the organs. The adrenaline content of the peripheral organs increased after electric foot-shock and changed according to the time of day. The peak of the circadian rhythm appeared about 6 hours after the peak of the urinary adrenaline rhythm. These findings suggest that adrenaline in body organs plays some role in the responses of the sympathetic nervous system to stressful conditions or even to daily activities.     

Alamethicin channel kinetics: Studies using fluctuation analysis and multifractal fluctuation analysis

The kinetics of the alamethicine channel incorporated into BLM was studied using detrended fluctuation analysis and multifractal detrended fluctuation analysis. Detrended fluctuation analysis has shown that both the event series formed with dwell times on fixed channel conductivity levels and the event series formed with opened states on all channel conductivity levels are random processes. However, multifractal detrended fluctuation analysis indicated that only dwell times series on fixed channel conductivity levels are random, but the event series formed with opened states on all channel conductivity levels are the correlated multifractal processes.