Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme

Molecular dynamics simulations of triclinic hen egg white lysozyme in aqueous solution were performed to calculate the intrinsic pK_as of 14 ionizable residues. An all-atom model was used for both solvent and solute, and a single 180 ps simulation in conjunction with a Gaussian fluctuation analysis method was used. An advantage of the Gaussian fluctuation method is that it only requires a single simulation of the system in a reference state to calculate all the pK_as in the protein, in contrast to multiple simulations for the free energy perturbation method. pK_int shifts with respect to reference titratable residues were evaluated and compared to results obtained using a finite difference Poisson-Boltzmann (FDPB) method with a continuum solvent model; overall agreement with the direction of the shifts was generally observed, though the magnitude of the shifts was typically larger with the explicit solvent model. The contribution of the first solvation shell to the total charging free energies of the titratable groups was explicitly evaluated and found to be significant. Dielectric shielding between pairs of titratable groups was examined and found to be smaller than expected. The effect of the approximations used to treat the long-range interactions on the pK_int shifts is discussed. © 1994 Wiley-Liss, Inc.     

Sensorimotor transformation from light reception to phototactic behavior inDrosophila larvae (Diptera: Drosophilidae)

In this paper we examine theDrosophila melanogaster larval response to light. We survey the morphology of the larval visual and motor systems in relation to larval locomotory behavior and phototaxis. In addition, this paper proposes a model of sensorimotor transformation and examines the reversal in taxis occurring at theD. melanogaster larval wnadering stage.     

Seasonal growth activity of local and foreign gracilarioid strains in Israel

Six gracilarioid strains originating from different climatical environments were cultured in two cultivation systems: a short-term indoor one with a cross gradiant table, and a long-term outdoor one. Seasonal growth performances of the different strains were determined. The growth results in the two culture systems showed similar trends. The tropical species.Gracilaria cornea andG. cornea mutant, showed highest growth rates during summer and no growth at all during winter. The temperate species,Gracilaria verrucosa andGracilariopsis lemaneiformis, showed best growth performances during winter with small fluctuations between seasons. The subtropical speciesGracilaria conferta (local) showed seasonal growth fluctuations all over the year. The foreign species definitely did not acclimate under local conditions, but successfully preserved their original response to temperature. Regression equations confirmed that temperature was the dominant environmental variable in most of the gracilarioid strains. The growth rate results obtained showed encouraging prospects for high algal productivity as compared to other cultivation systems. Seasonal cultivation strategy ofGracilaria spp. in Israel is discussed.     

Thermostable β-Glycosidase from Sulfolobus Solfataricus

The Sulfolobus solfataricus β-glycosidase (Sβgly) is a thermostable and thermophilic glycosyl-hydrolase with broad substrate specificity. The enzyme hydrolizes β-D-gluco-, fuco-, and galactosides, and a large number of /Winked glycoside dimers and oligomers, linked β1-3, β1-4, and β1-6, It is able to hydrolize oligosaccharides with up to 5 glucose residues. Furthermore, it is also able to promote transglycosylation reactions. The corresponding gene has been cloned and overexpressed both in yeast and Escherichia coli. Based on sequence and functional data, the Sβgly has been assigned to the so-called BGA family of glycosyl-hydrolases, including β-glycosidases, β-galactosidases and phosho-β-galactosidases from mesophilic and thermophilic organisms of the three domains. The Sβgly has been crystallized and the resolution of its structure is in progress. Because of its special properties, the enzymes has considerable biotechnological potential.     

Electron microscope tomography of Balbiani Ring hnRNP substructure

Three-dimensional (3-D) reconstructions, by electron microscope tomography, of selectively stained, contrast enhanced Balbiani Ring (BR) hnRNP granules reveal a complex spatial arrangement of RNA-rich domains. This particulate substructure was examined by volume rendering computer graphics. Modeling the arrangement of RNA-rich domains is made difficult by apparent structural flexibility and/or heterogeneity of composition. Formulation of a consensus 3-D arrangement of RNA-rich domains will require an expanded data base of reconstructed BR granules and the development of new image manipulation and analysis techniques. This study demonstrates the potential for ultra-structural cell biology of combining several new techniques: selective nucleic acid staining, electron spectroscopic imaging to enhance contrast, electron microscope tomography and volume rendering computer graphics.Abbreviations BR Balbiani Ring - EMT electron microscope tomography - ESI electron spectroscopic imaging - hnRNP heterogeneous nuclear ribonucleoprotein - OA-B osmium ammine-B - kb kilobases by P.B. Moens     

Mould growth and conidiation in cereal grains as affected by water activity and temperature

The effects of different water activities ( a _w) and temperatures on growth of storage moulds ( Aspergillus candidus and Penicillium implicatum ) on maize and paddy rice grains were measured using ergosterol content and dilution plating. The results showed that the mode of fungal growth depends on a _w. In all cases, conidiation occurred more readily at low a _w, whereas mycelial growth is more marked at higher a _w. The xerotolerant, thermophilic characteristics of A. candidus were more clearly revealed by the ergosterol content, which reflected mycelial development, than by enumeration of spores formed. The ergosterol content proved to be a better index of technological quality of cereals (assessed by acidity) than the number of fungal propagules. A 10-fold increase in the number of spores corresponded to a doubling of the ergosterol content.     

The dynamics of sparse random networks

Recurrent neural networks with full symmetric connectivity have been extensively studied as associative memories and pattern recognition devices. However, there is considerable evidence that sparse, asymmetrically connected, mainly excitatory networks with broadly directed inhibition are more consistent with biological reality. In this paper, we use the technique of return maps to study the dynamics of random networks with sparse, asymmetric connectivity and nonspecific inhibition. These networks show three qualitatively different kinds of behavior: fixed points, cycles of low period, and extremely long cycles verging on aperiodicity. Using statistical arguments, we relate these behaviors to network parameters and present empirical evidence for the accuracy of this statistical model. The model, in turn, leads to methods for controlling the level of activity in networks. Studying random, untrained networks provides an understanding of the intrinsic dynamics of these systems. Such dynamics could provide a substrate for the much more complex behavior shown when synaptic modification is allowed.     

Novel thieno[2,3-b]- and [3,4-b]pyrans as potassium channel openers. Thiophene systems—XVII

The syntheses and antihypertensive activity of the thieno[3,4-b]pyran and thieno[2,3-b]pyran isosteres of the potassium channel opener (PCO) RWJ 26629 (± 2a) are reported. While the unsubstituted thiophene derivatives were active at 20 mg/kg, introduction of a strong electron withdrawing group in the 2-position of the thieno[3,2-b] series increased potency. Similar substitution on the thieno[3,4-b] series significantly lowered potency. Compounds 26 and 30 are approximately 5-fold more potent than the prototypic PCO cromakalim (± 1).