Prediction of the packing arrangement of strands in β-sheets of globular proteins

A method is proposed for predicting the adjacency order in which strands pack in a -sheet in a protein, on the basis of its amino acid sequence alone. The method is based on the construction of a predicted contact map for the protein, in which the probability that various residue pairs are close to each other is computed from statistically determined average distances of residue pairs in globular proteins of known structure. Compact regions, i.e., portions of the sequence with many interresidue contacts, are determined on the map by using an objective search procedure. The proximity of strands in a -sheet is predicted from the density of contacts in compact regions associated with each pair of strands. The most probable -sheet structures are those with the highest density of contacts. The method has been tested by computing the probable strand arrangements in a five-strand -sheet in five proteins or protein domains, containing 62–138 residues. Of the theoretically possible 60 strand arrangements, the method selects two to eight arrangements as most probable; i.e., it leads to a large reduction in the number of possibilities. The native strand arrangement is among those predicted for three of the five proteins. For the other two, it would be included in the prediction by a slight relaxation of the cutoff criteria used to analyze the density of contacts.     

The effect of age on lipid composition and order of rat cerebral microvessels

To determine if alterations in lipid composition and/or membrane order of cerebral microvessels may contribute to the age-related changes in blood-brain barrier (BBB) function, cerebral microvessels isolated from male Fischer 344 rats at 3 (young), 12 (intermediate age), and 24 (aged) months of age were studied. The steady state fluorescence polarization of diphenylhexatriene incorporated into isolated cerebral microvessel membranes at 35°C, in aged rats was not different compared to young rats (0.2787±0.0029 vs 0.2847±0.0049). In addition, the thermotropic transition temperature of these membranes was not altered with age. Moreover, the fatty acid composition, the double bond index as well as cholesterol to phospholipid molar ratios were not significantly altered with age. In contrast, the concentration of conjugated dienes in lipid extracts of cerebral microvessels of aged rats (10.04±1.10 O.D./mg phospholipids) was significantly increased compared to the concentration in young rats (6.98±0.52 O.D./mg phospholipids) (p<0.01). It is concluded that aging is not associated with significant changes in lipid composition or membrane order of cerebral microvessels. However, the increased concentration of conjugated dienes in cerebral microvessels of aged rats is indicative of ongoing free radical damage in these microvessels which may contribute to the age-related changes in BBB function.     

Voluntary progression order in captive rhesus macaques

The sequence in which 14 laboratory rhesus macaques left their home enclosure during a routine catching procedure was recorded on 30 occasions during 6 weeks. The animals were trained to voluntarily exit one by one and enter a transport cage for weighing and/or treatment. Mean weekly exit orders cross-correlated significantly, and individuals retained their exit positions with remarkable consistency throughout the study period. An animal's position did not depend on its sex, age, or dominance rank. The oldest female never failed to enter the transport cage as number 1. When she was prevented from taking the lead, the group was hesitant but eventually proceeded in the usual order. Food was a strong, yet not absolute, incentive for the monkeys to cooperate. If they could not expect a reward, they took more time before proceeding, but did so in the habitual order. The predictability of the exit sequence has practical managerial value because it makes it possible for a single person to quickly catch a selected group member when necessary.     

Vegetation succession on the dunes near Oostvoorne,The Netherlands,since 1934, interpreted from air photographs and vegetation maps

The vegetation succession on the dunes near Oostvoorne, The Netherlands has been followed by means of a novel combination of repeated large-scale vegetation mapping and air photograph interpretation. Vegetation units have been discerned on the formation level because these could be distinguished fairly easily on the photographs and because the rates of change are appropriate to the time interval chosen. Nineteen formations were distinguished. Five 1:6250 maps were constructed, reflecting the formation pattern in 1934, 1943, 1959, 1972 and 1980. An overlay with 2736 grid points at 25 m field distance was used to quantify changes in the formation pattern.The results suggest a pronounced multiple pathway succession with nevertheless three principal trajectories of succession from pioneer to woodland vegetation. The outer dunes, which have originated since 1910, are distinct in successional characteristics from the inner dunes, which already existed but were released from heavy grazing pressure in 1910. The rate of change in the outer dunes was high in the beginning and is slowly decreasing eversince. In the inner dunes it went the other way around. Through visual extrapolation the likely formation patterns in 1910 and in 2000 were estimated.Transition frequencies proved highly variable for most formations. Moreover, strong spatial dependence was found. Limitations in the use of Markov models in cases of long-term succession in heterogeneous environments are discussed.Nomenclature follows the same sources as in van der Maarel et al. (1984).Field work carried out 1980–1981 when the authors were at the Division of Geobotany, University of Nijmegen. We thank Jos Rijntjes, Nijmegen, for his cooperation in the field. Vegetation maps were prepared and calculations performed at Uppsala. We thank the Foundation Het Zuid-Hollands Landschap, Rotterdam, for providing facilities and a grant for fieldwork as well as additional means to reproduce the vegetation maps. Two reviewers gave useful comments.     

Modulation of locomotor activity by substance P in rats

The effects of intraperitoneally or intracerebrally (DA A-10 area) administered substance P (SP) on locomotor activity of rats were studied in an exact 12-h light/12-h dark cycle changing from dark to light at 6 a.m. SP was administered either at 11 a.m. (light phase, minimal locomotor activity) or at 7 p.m. (dark phase, maximal locomotor activity). The effects of 12.5 micrograms/kg SP intracerebral and 125 micrograms/kg SP intraperitoneal were very similar. In the light phase SP produces excitation but inhibition of locomotion in darkness. Hence, the effect of SP depends on the internal mechanisms controlling motor activity and tends to level off the spontaneous circadian oscillation. We found a long lasting SP effect during both the light and dark period. The present experiments led us to the conclusion that SP has a levelling effect on locomotor activity. Probably this effect might be explained as SP's action on the dopaminergic pathway or dopamine metabolism, because the dopamine content in neurons also has a circadian rhythm.     

Modulation of the orientational order profile of the lipid acyl chain in the Lα phase

The orientational order profile along the lipid acyl chain has been characterized under several different conditions of polar headgroup composition, temperature, and cholesterol content. Despite the different nature of these factors, the variation of the order is governed by two common trends. First, the relative change of order induced by the variation of these factors is always more pronounced towards the end of the chain than for the methylene groups near the interface. Second, there is, to a first approximation, a distinct correlation between the magnitude of the order parameters and the shape of the order profile. For example when the chain is highly ordered, the relative width of the order distribution is narrow indicating that the plateau region is longer. These conclusions suggest that the orientational order profile depends on only a small number of parameters and demonstrate clearly that the correlation length for changes in orientational order is much greater than one C-C bond length. Our results also show that the reduced temperature is not related in simple terms to orientational order and probably has little theoretical significance. The orientational order profiles of POPC and POPE bilayers are significantly different even when expressed in terms of reduced temperature. The behavior of POPC/cholesterol systems also indicates that the orientational order of the lipid chain and the gel-to-liquid crystalline phase transition temperature are not related in a straightforward manner.Abbreviations POPC 1-palmitoyl-2-oleoyl-phosphatidylcholine - POPE 1-palmitoyl-2-oleoyl-phosphatidylethanolamine - PC phosphatidylcholine - PE phosphatidylethanolamine - NMR nuclear magnetic resonance - EDTA ethylenediaminetetraacetic acid Offprint requests to: M. Bloom     

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.     

Collective motions in proteins investigated by X-ray diffuse scattering

We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 Å, as well as to changes of the functional form of the correlation function. (3) But only the “average” value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe. © 1994 John Wiley & Sons, Inc.     

Investigation of the enantioselectivity and enantiomeric elution order of some piperidine-2,6-dione drugs on chiralcel OD column

The enantioselectivity and enantiomeric separation of five racemic piperidine-2,6-dione compounds, on the cellulose tris(3,5-dimethylphenyl carbamate) chiral stationary phase Chiralcel OD-CSP were investigated under the same chromatographic conditions. This class of drugs includes glutethimide, aminoglutethimide, cyclohexylaminoglutethimide, pyridoglutethimide, and phenglutarimide. The results revealed that chiral recognition and the binding sites of these drugs on the Chiralcel OD column are similar, regardless of the absolute configuration of the individual enantiomers. A possible chiral recognition mechanism(s) for this class of drugs and the CSP is presented. © 1994 Wiley-Liss, Inc.     

A theory of evaluation applied to human-environment systems

1. 1. The writers present the general theory of evaluation that is being developed by their group.

2. 2. The evaluation of a human environment is a complex mental process.

3. 3. In an effort to express numerically the quality of an environment, one tends to oversimplify the complex aspects of it and the entailing problems in relation to its inhabitants.

4. 4. In this paper, some examples are taken in the evaluation of thermal environments, wherein much has been said and done in setting up numerical scales to express human comfort, and yet neither clear-cut explanations nor convincing logic seem to exist to terminate the argument over the widely scattered and sometimes seemingly contradicting experimental data.

5. 5. The writers suggest that many of the reasons for this confusion may be traced back to the oversimplified notion of evaluation.

6. 6. It is shown that there are various possibilities when looking at the scales of evaluation.

7. 7.|The nominal scale, least studied of all the four traditional scales, may be given a prominent place in evaluating a thermal environment. The pseudo-interval order scale is another example.