Improved molecular dynamics simulations for the determination of peptide structures

In this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents highlighted. A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers). Lastly, a penalty term for coupling constants directly related to the Karplus curve has been plemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained. © 1993 John Wiley & Sons, Inc.     

Dynamic concentration challenges for biosensor characterization

A method and apparatus are described for characterization of the steady state and dynamic response of biosensors. The apparatus produces a steady stream of homogeneously mixed analyte whose concentration can be fixed at discrete values or varied continously. The device is ideally suited for continously operated biosensors, but is also effective for biosensors that operate in discrete sampling modes. The system permits simultaneous testing of several sensors and determination of the accuracy, precision and repeatability of sensor response. The characteristics of this testing apparatus were validated with ferrocyanide and glucose as indicators. As an example of use of the apparatus, concentration ramps were created and used to complement conventional step changes for characterizing an implantable glucose sensor. The ramp rate can be adjusted easily by scaling the apparatus to simulate the rate of concentration change anticipated during actual monitoring situations.     

COEXLSTENCE OF TOXIC AND NONTOXIC DINOKLAGELLAIES RESEMBLING GQNYAULAX TAMARENSIS IN NEW ENCILAND COASTAL WATERS (NW ATLANTIC)1

Two forms resembling Gonyaulax tamarrensis Lebour coexist in Maine cosat plankton; one is toxic, the other is nontoxic. At times, red patches of dinoflagellates were identified as G. tamarensis, yet only presumed to he toxic. Toxic froms were found in June, July 1975 and 1976. The nontoxic form was found in a more esraurine area, e.g., mid-July 1975, early July 1976. These two forms are not easily distinguished by conventional microncopic ohservation, nor by pigment analysis. Preliminary observations suggest that the nontoxic form is smaller than G. excavata (Braarud) Balech and tacks the “excavated” ventrat region. Characteristic G. excavata resting cysts were found in sediment from the shellfish toxic area off Newagen and Monhegan (Maine) and were not found in sediments from areas where the nontoxic form bloomed. There appear to be a minimum of two G. tamarensis-like organisms. Full systematic treatment of these must await further information.     

On the natural occurrence of gossypetin 7- and 8-monomethyl ethers

The 7-methyl ether of gossypetin occurs, as a mixture of 4 glycosides, in the yellow inflorescence of Eriogonum nudum. In contrast to previous reports, however, it does not occur in Lotus corniculatus flowers, nor is it present in leaves of Medicago sativa. The 8-methyl ether, which is present in Lotus flowers, has been found for the first time in the Compositae, in flowers of Geraea canescens.     

Facilitation of suction termination using extra-amniotic prostaglandins in gel

Extra-amniotic prostaglandin E₂ (PGE₂) suspended in a slow release gel (Tylose) was instilled in 35 patients prior to a planned surgical termination in an attempt to dilate the cervix, minimize cervical trauma, and reduce the possible risk of cervical incompetence and its sequelae. Dilatation occurred in all patients to a minimum of 8 mm and 74% aborted before surgical evacuation performed 6 to 24 hours after injection. No serious side effects occurred. Extra-amniotic PGE₂ in gel should be considered as a primary procedure when the cervix is obviously immature on examination. If the cervix is found to be tight and unyielding at surgical dilatation, the latter procedure should be discontinued and PGE₂ in gel injected.     

Evidence of a precursor form of stratum corneum basic protein in rat epidermis.

The fully differentiated anucleate cells of the stratum corneum of newborn rat epidermis contain a cationic protein called stratum corneum basic protein (SCBP). This protein has a molecular weight (49 000) and an amino acid composition similar to a protein extracted from the less differentiated cell layers of the epidermis. Pulse--chase experiments with radiolabeled histidine were undertaken to test the possiblity that SCBP is derived from a preexisting protein. A protein of 52 000 daltons is rapidly but transiently labeled in extracts of the less differentiated cell layers. As the amount of label in the 52 000-dalton protein decreases, an increase in radiolabel is observed in extracts of the fully differentiated cells. This label is found in SCBP, a protein of lower molecular weight (49 000) than that initially labeled. These proteins are immunologically related and both are resistant to cyanogen bromide cleavage. They differ in apparent molecular weight on sodium dodecyl sulfate--polyacrylamide gels and in their net charge. The results are consistent with the conversion of a precursor protein into SCBP.     

Induced tillering ofLolium multiflorum in vitro

Four growth regulators incorporated into Murashige and Skoog's basal medium were tested for their effect on the rate of tillering ofLolium multiforum plantlets in culture. Tillering was stimulated in the presence of 1–2 mg l⁻¹ 6-benzylaminopurine, but 1 mg l⁻¹ gave less plantlet distortion and the tillers could be separated easily. Small shoot tips were considered to be best for establishing aseptic cultures for propagation, but individual tillers were best for transferring to the tiller inducing medium, both initially and at subculturing. Tillering rate was affected by culture vessel, temperature and light intensity. Of the variations tested, the optimum conditions were to culture whole tillers onto a medium containing 1 mg l⁻¹ BAP in 30-ml universal tubes at 20°C with continuous white fluorescent light at 12,000 lx for 4–5 weeks. Rates in excess of 40 tillers per month were obtained in culture compared with 5–12 in the glasshouse.     

The dimeric nature of an R-factor mediated β-lactamase

The molecular weight of the β-lactamase mediated by R46 as determined by SDS-gel electrophoresis is about half that of the native enzyme, indicating the presence of subunits. Similar evidence for subunits was found with the β-lactamase mediated by R55. $\text{In}\text{vivo}$ hybridization occurred between the R46 and R55 β-lactamases.     

Cell growth and death rates as factors in the long-term performance, modeling, and design of immobilized cell reactors

The viable fraction of immobilized cells in a bioreactor may be critical in predicting long-term or steady-state reactor performance. The assumption of near 100% viable cells in a bioreactor may not be valid for portions of immobilized cell reactors (ICRs) characterized by conditions resulting in appreciable death rates. A mathematical model of an adsorbed cell type ICR is presented in which a steady-state viable cell fraction is predicted, based on the assumptions of no cell accumulation in the reactor and a random loss of cells from the reactor. Data on cell death rates, cell growth rates, and productivity rates as functions of temperature, substrate, and ethanol concentration for the lactose utilizing yeast K. fragillis were incorporated into this model. The steady-state reactor viable cell fraction as predicted by this model is a strong function of both temperature and ethanol concentration. For example, a stable 20% viable fraction of the immobilized cells is predicted in ICR locations experiencing continuous conditions of either 30 g/L ethanol at 40 degrees C, or 95 g/L ethanol at 25 degrees C. Steady-state ICR "plug flow" concentration profiles and column productivities are predicted at three operating temperatures, 20, 30, and 40 degrees C using two different models for ethanol inhibition of productivity. These profiles suggest that the reactor operating temperature should be low if higher outlet ethanol concentrations are desired. Three reactor design strategies are presented to maximize the viable cell fraction and improve long-term ethanol productivity in ICR's: (1) reducing outlet ethanol concentrations, (2) rotating segments of an ICR between high and low ethanol environments, and (3) simultaneous removal of the ethanol produced from the reactor as it is formed.