Computational analysis of chain flexibility and fluctuations in Rhizomucor miehei lipase.

We have performed molecular dynamics simulation of Rhizomucor miehei lipase (Rml) with explicit water molecules present. The simulation was carried out in periodic boundary conditions and conducted for 1. 2 ns in order to determine the concerted protein dynamics and to examine how well the essential motions are preserved along the trajectory. Protein motions are extracted by means of the essential dynamics analysis method for different lengths of the trajectory. Motions described by eigenvector 1 converge after approximately 200 ps and only small changes are observed with increasing simulation time. Protein dynamics along eigenvectors with larger indices, however, change with simulation time and generally, with increasing eigenvector index, longer simulation times are required for observing similar protein motions (along a particular eigenvector). Several regions in the protein show relatively large fluctuations and in particular motions in the active site lid and the segments Thr57-Asn63 and the active site hinge region Pro101-Gly104 are seen along several eigenvectors. These motions are generally associated with glycine residues, while no direct correlations are observed between these fluctuations and the positioning of prolines in the protein structure. The partial opening/closing of the lid is an example of induced fit mechanisms seen in other enzymes and could be a general mechanism for the activation of Rml.     

Consumption rates and food preferences of slugs in a calcareous grassland under current and future CO<Subscript>2</Subscript> conditions

This study explored consumption of a generalist herbivore feeding on leaf tissue of various plant species of a calcareous grassland, and tested whether consumption levels and preferences changed when plants were exposed to 5 years of in situ CO₂ enrichment. The first part of this experiment tested whether the consumption patterns of slugs (Deroceras reticulatum) observed in single-species feeding tests were altered when slugs were given a choice of food sources. Overall consumption increased 270% when slugs were given a choice, and they preferred having a choice of food sources more than they preferred having any one food source. Surprisingly, slugs consumed fewer legumes and grasses and more non-leguminous forbs when given a choice. In the second part of this experiment, feeding behaviors of slugs in response to elevated CO₂ were investigated by feeding them leaves of two legumes, one grass, and a non-leguminous forb (Trifolium medium, Lotus corniculatus, Bromus erectus, and Sanguisorba minor, respectively) in two or four species combinations. In the leguminous species mix, the non-leguminous species mix, and the combined mix (legumes and non-legumes), neither overall consumption by herbivores nor species preference was significantly altered by long-term CO₂ enrichment. In the combined species mix, slugs preferred legumes to non-legumes (P=0.012) and exhibited a weak functional group preference shift from non-legumes to legumes (P=0.089) in response to CO₂ enrichment. This is the first time such a shift has been observed, and provides evidence that there may be multiple herbivore responses to rising atmospheric CO₂ concentrations. Numerous single-species feeding tests using insects have shown that consumption by herbivores may increase when herbivores are fed plants grown in enriched CO₂ atmospheres. This study clearly demonstrates the limited applicability of non-choice feeding trials to generalist herbivores in species-rich communities. Received: 19 August 1999 / Accepted: 20 April 2000     

The interaction of general anaesthetics and neurosteroids with GABA(A) and glycine receptors.

The positive allosteric effects of four structurally distinct general anaesthetics (propofol, pentobarbitone, etomidate and 5alpha-pregnan-3alpha-ol-20-one [5alpha3alpha]) upon recombinant GABA(A) (alpha6beta3gamma2L), invertebrate GABA (RDL) and glycine (alpha1) receptors expressed in Xenopus laevis oocytes have been determined. Propofol and pentobarbitone enhanced agonist (GABA or glycine as appropriate) evoked currents at GABA(A), glycine, and RDL receptors, whereas etomidate and 5alpha3alpha were highly selective for the GABA(A) receptor. Utilizing site-directed mutagenesis, we demonstrate that the nature of the interaction of propofol, pentobarbitone and etomidate (but not 5alpha3alpha) with mammalian and invertebrate ionotropic GABA receptors depends critically upon the nature of a single amino acid located in the second transmembrane region (TM2) of these receptors. These data are discussed in relation to the specificity of action of general anaesthetics.     

Modeling the hypothalamus–pituitary–adrenal system: homeostasis by interacting positive and negative feedback

The hypothalamus–pituitary–adrenal (HPA) system is closely related to stress and the restoration of homeostasis. This system is stimulated in the second half of the night, decreases its activity in the daytime, and reaches the homeostatic level during the late evening. In this paper, we derive and discuss a novel model for the HPA system. It is based on three simple rules that constitute a principle of homeostasis and include only the most substantive physiological elements. In contrast to other models, its main components include, apart from the conventional negative feedback ingredient, a positive feedback loop. To validate the model, we present a parameter estimation procedure that enables one to adapt the model to clinical observations. Using this methodology, we are able to show that the novel model is capable of simulating clinical trials. Furthermore, the stationary state of the system is investigated. We show that, under mild conditions, the system always has a well-defined set-point, which reflects the clinical situation to be modeled. Finally, the computed parameters may be interpreted from a physiological point of view, thereby leading to insights about diseases like depression, obesity, or diabetes.