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PubMed1985

Analysis of the factors and implications of an empirical method for estimating the stability of mutant human haemoglobins.

An empirical method for estimating the effects of single amino acid substitutions on structural stability of proteins with known spatial structure is developed. Twenty physical and chemical properties of amino acids and characteristics of protein tertiary structure were analysed to determine those most involved in producing instability. We employed data on 330 mutant variants of the alpha- and beta-subunits of human haemoglobin in choice of the parameters of the method developed which yielded a 81% of prediction accuracy of stability estimates for human mutant haemoglobins.

Amino Acid Sequence↗
PubMed2005

Spatiotemporal dynamics in marginal populations.

Population dynamics across a mortality gradient at an ecological margin are investigated using a novel modeling approach that allows direct comparison of stochastic spatially explicit simulation results with deterministic mean field models. The results show that demographic stochasticity has a large effect at population margins such that density profiles fall off more sharply than predicted by mean field models. Substantial spatial structure emerges at the margin, and spatial correlations (measured parallel to the margin) exhibit a sharp maximum in the tail of the density profile, indicating that spatial substructuring is greatest at an intermediate point across the ecological gradient. Such substructuring may have a substantial impact on Allee effects and evolutionary processes in marginal populations.

Animals↗
PubMed2003

Strategy of computer-aided drug design.

Modern strategies of computer-aided drug design (CADD) are reviewed. The task of CADD in the pipeline of drug discovery is accelerating of finding the new lead compounds and their structure optimization for the following pharmacological tests. The main directions in CADD are based on the availability of the experimentally determined three-dimensional structure of the target macromolecule. If spatial structure is known the methods of structure-based drug design are used. In the opposite case the indirect methods of CADD based on the structures of known ligands (ligand-based drug design) are used. The interrelationship between the main directions of CADD is reviewed. The main CADD approaches of molecule de novo design and database mining are described. They include methods of molecular docking, de novo design, design of pharmacophore and quantity structure-activity relationship models. New ways and perspectives of CADD are discussed.

Computational Biology↗
PubMed1993

Spatiotemporal organization of simple-cell receptive fields in the cat's striate cortex. I. General characteristics and postnatal development.

1. Most studies of cortical neurons have focused on the spatial structure of receptive fields. For a more complete functional description of these neurons, it is necessary to consider receptive-field structure in the joint domain of space and time. We have studied the spatiotemporal receptive-field structure of 233 simple cells recorded from the striate cortex of adult cats and kittens at 4 and 8 wk postnatal. The dual goal of this study is to provide a detailed quantitative description of spatiotemporal receptive-field structure and to compare the developmental time courses of spatial and temporal response properties. 2. Spatiotemporal receptive-field profiles have been measured with the use of a reverse correlation method, in which we compute the cross-correlation between a neuron's response and a random sequence of small, briefly presented bright and dark stimuli. The receptive-field profiles of some simple cells are space-time separable, meaning that spatial and temporal response characteristics can be dissociated. Other cells have receptive-field profiles that are space-time inseparable. In these cases, a particular spatial location cannot be designated, unambiguously, as belonging to either an on or off subregion. However, separate on and off subregions may be clearly distinguished in the joint space-time domain. These subregions are generally tilted along an oblique axis. 3. Our observations show that spatial and temporal aspects of receptive-field structure mature with clearly different time courses. By 4 wk postnatal, the spatial symmetry and periodicity of simple-cell receptive fields have reached maturity. The spatial extent (or size) of these receptive fields is adult-like by 8 wk postnatal. In contrast, the response latency and time duration of spatiotemporal receptive fields do not mature until well beyond 8 wk postnatal. 4. By applying Fourier analysis to spatiotemporal receptive-field profiles, we have examined the postnatal development of spatial and temporal selectivity in the frequency domain. By 8 wk postnatal, spatial frequency tuning has clearly reached maturity. On the contrary, temporal frequency selectivity remains markedly immature at 8 wk. We have also examined the joint distribution of optimal spatial and temporal frequencies. From 4 wk postnatal until 8 wk postnatal, the range of optimal spatial frequencies increases substantially, whereas the range of optimal temporal frequencies remains largely unchanged. From 8 wk postnatal until adulthood, there is a large increase in optimal temporal frequencies for cells tuned to low spatial frequencies. For cells tuned to high spatial frequencies, the distribution of optimal temporal frequencies does not change much beyond 8 wk postnatal.(ABSTRACT TRUNCATED AT 400 WORDS)

Aging↗
PubMed1993

Phyletic relationships of protein structures based on spatial preference of residues.

A structure-based scoring matrix MDPRE was derived from amino acid spatial preferences in protein structures. Sequence alignment and evolutionary studies by using MDPRE matrix gave similar results as those from ordinary sequence and structure alignments. It is interesting that a matrix derived from structure data solely could give comparable alignment results, strongly indicating the intimate connection between protein sequences and structures. The branch order and length from this approach were close to those obtained by a structure comparison method. Thus, by applying this structure-based matrix, the trees obtained should reflect evolutionary characteristics of protein structure. This approach takes advantage over a direct structure comparison in that (1) only a sequence and MDPRE matrix are needed, making it simple and widely applicable (especially in the absence of 3-dimensional protein structure data); (2) an established algorithm for sequence alignment and tree building could be employed, providing opportunities for direct comparison between matrices from different methodologies. One of the most striking features of this method is its capability to detect protein structure homologies when the sequence identities are low. This was well reflected in the given examples of the alignment of dinucleotide-binding domains.

Amino Acid Sequence↗
PubMed1997

Visualization of a calcium hydroxylapatite molecular structure.

The creation of the three-dimensional complex spatial structure, and peculiarity of changes occurring in a material, because of external influence. The algorithm of the volumetric (space-filling) and ball-pivot model of molecules images construction applied in the system, allows to display ball-pivot and volumetric models of molecules movement in real time scale. Pseudo-three-dimensional image of a molecule, allowing a good look at it from the different points of view, is formed and the opportunity of the stereoimage creation increases presentation effect of its volume many times. The work contains the standard crystal lattice parameters account method of a calcium hydroxylapatite based on the rontgenogram of the material samples. The summary table of Cartesian coordinates of atoms of a calcium hydroxylapatite is applied.

Biocompatible Materials↗
PubMed1986

Spatial receptive-field properties of direction-selective neurons in cat striate cortex.

Responses of direction-selective neurons in cat striate cortex (area 17) were studied with flashed-bar stimuli. Spatial parameters of interactions within the receptive field giving rise to direction selectivity and of receptive-field subunits were quantitatively determined for the same cells and correlated. A bar stimulus flashed sequentially at two nearby locations in the receptive field produced direction-selective behavior comparable with that elicited by continuously moving stimuli. Each cell exhibited a characteristic optimal spatial displacement, Dopt, for which responses in the presumed preferred and null directions were maximally distinct. In all cases, Dopt was much smaller than the receptive-field size. The spatial structure of receptive fields in simple cells was studied using single narrow-bar stimuli flashed at different locations in the receptive field. The resulting line-weighting function exhibited alternating regions of ON and OFF responses having a characteristic spatial period or wavelength, lambda. Spatial subunit structure in complex cells was determined by flashing two bars simultaneously in the receptive field. The response as a function of bar separation was again a wavelike function having a spatial wavelength, lambda. Values of the optimal displacement for direction selectivity, Dopt, showed a clear relationship with the spatial wavelength, lambda, for a given unit. Dopt was also correlated to a somewhat lesser degree with receptive-field size. Generally, the ratio of Dopt to lambda was approximately 1/10 to 1/4, in agreement with theoretical predictions by Marr and Poggio. Taken together with the findings of Movshon et al., these results indicate a systematic relationship between Dopt and the spatial frequency of a sinusoidal grating, which is optimal for that cell. Such a relationship is consistent with the results of human psychophysical experiments on apparent motion.

Animals↗
PubMed1992

Primary structure of carboxypeptidase T: delineation of functionally relevant features in Zn-carboxypeptidase family.

The primary structure of carboxypeptidase T--a Zn-dependent extracellular enzyme of Thermoactinomyces vulgaris--was determined from the cloned cpT gene nucleotide sequence and compared to Zn-carboxypeptidases from various organisms. The compilation and analysis of multiple alignment accompanied by consideration of available tertiary structure data have shown that in the overall spatial structure and active site arrangement CpT is similar to other enzymes constituting the Zn-carboxypeptidase family. Nine of 16 amino acid residues found to be strictly invariant are presumably located close to the active site. The preservation of His69, Glu72, Asn144, Arg145, His196, Tyr248, and Glu270 identified previously as essential catalytic site participants implicates basically the same catalytic mechanism in the Zn-carboxypeptidase family. It is proposed that Pro205 and Asp256 should play an important role in proper S1'-pocket spatial arrangement. The comparative analysis of amino acid variations in S1'-pocket enabled us to reveal structural determinants of the Zn-carboxypeptidase primary specificity. The relatively reduced size of the pocket and negative charge of Asp253 are supposed to contribute correspondingly to A- and B-type substrate preferences of carboxypeptidase T endowed with dual primary specificity.

Amino Acid Sequence↗
PubMed1999

Genetic variability in sensitivity to population density affects the dynamics of simple ecological models.

Many 1-dimensional discrete time ecological models contain a sensitivity parameter that does not affect the dynamic complexity of these models. We show that genetic variability in this parameter can have a strong effect on population dynamics. We incorporate ecological dynamics in two different population genetic models with one locus and two alleles. The first is the classical model of a randomly mating population in Hardy-Weinberg equilibrium, and the second is a model of differential selection in males and females. In populations in Hardy-Weinberg equilibrium, variability in the sensitivity parameter can be maintained by overdominance. In this case, the dynamics of the polymorphic population tend to be much simpler than those of monomorphic populations. In the model with different selection in males and females, polymorphisms can be maintained in various ways, e.g., by opposing directional selection in males and females. Polymorphism in the sensitivity parameter tends to simplify population dynamics in the model with different selection in males and females as well. A number of interesting dynamic effects can be observed, e.g., multiple attractors with complicated basins of attraction. Then the final state of the system after a successful invasion by mutant alleles may depend on the mutation rate and on the distribution of mutational steps. In addition, there are situations in which genetic variability destabilizes a stable population dynamic equilibrium in the monomorphic model. There is an analogy between genetic variability and variability imposed by the environment. If differences in sensitivity are caused by the environment, dynamic effects similar to those in the genetic models can be observed. In addition, source-sink structures that are known to occur in spatially structured models can be seen in the genetic model if one of the genotypes is inviable. The results suggest that combining ecological and population genetic models can lead to a number of new insights. More work is needed, e.g., with fertility models, in which fitnesses are not assigned to individuals, but to mating pairs.

Alleles↗
PubMed2005

Bayesian hierarchical modelling to enhance the epidemiological value of abattoir surveys for bovine fasciolosis.

Four classes of Bayesian hierarchical models were evaluated using an historical dataset from an abattoir survey for fasciolosis conducted in Victoria, Australia. The purpose of this analysis was to identify areas of high prevalence and to explain these in terms of environmental covariates. The simplest of the Bayesian models, with a single random effect, validated the use of smoothed maps for cartographic display when the sample sizes vary. The model was then extended to partition the random effect into spatially structured and unstructured components, thus allowing for spatial autocorrelation. Rainfall, irrigation, temperature-adjusted rainfall and a remotely sensed surrogate for rainfall, the normalised difference vegetation index (NDVI), were then introduced into the models as explanatory variables. The variable that best explained the observed distribution was irrigation. Associations between prevalence and both rainfall and NDVI that were significant in fixed effects models were shown to be due to spatial confounding. Nevertheless, provided they are used cautiously, confounded variables may be valid predictors for the prevalence of disease.

Abattoirs↗
PubMed2006

Manifestation of weak localization and long-range correlation in disordered wave functions from conical second harmonic generation.

We experimentally demonstrate that the near-field patterns of conical second harmonic generation of a laser in random domain structures can be used to explore the spatial structure of two-dimensional disordered wave functions with weak localization. The statistics of the experimental near-field patterns agree very well with the theoretical distributions. In addition to the short-range correlation, the localization effects are found to contribute a nearly constant value to the long-range correlation. The result of this Letter also confirms the possibility of using conical second harmonic generation as a diagnostic tool for topographical characterization of crystals.

Journal Article↗
PubMed1993

[Approach to the study of natural peptides from structure to functions. III. Structural organization of an adrenorphin molecule and its synthetic analogs].

Spatial structure of the peptide hormone adrenorphin was investigated by the theoretical conformational method. A solution of the "reverse conformational problem" for adrenorphin made it possible to predict a series of the modified synthetic analogues, which may assume one of the low-energy conformations of the native hormone.

Amino Acid Sequence↗
PubMed2002

Metapopulation structure of the specialized herbivore Macrosiphoniella tanacetaria (Homoptera, Aphididae).

We investigated population dynamics, genetic diversity and spatial structure in the aphid species Macrosiphoniella tanacetaria, a specialist herbivore feeding on tansy, Tanacetum vulgare. Tansy plants (genets) consist of many shoots (ramets), and genets are grouped in sites. Thus, aphids feeding on tansy can cluster at the level of ramets, genets and sites. We studied aphid population dynamics in 1997 and 2001 and found that within sites: (i). at any time, aphids used only a fraction of the available ramets and genets; (ii). at the level of ramets, most aphid colonies survived only one week; (iii). at the level of genets, mean survival time was less than 4 weeks; and (iv). colonization and extinction events occurred throughout the season. We sampled aphids in seven sites in the Alsace region, France (4-45 km apart) and two sites in Germany in 1999 to study genetic structure within and between populations. Genetic analyses using nine microsatellite loci showed that: (i). genotypic variability was high, (ii). none of the populations was in Hardy-Weinberg equilibrium, (iii). heterozygote deficits and linkage disequilibria were frequent, and (iv). all populations were genetically differentiated, even at a small geographical scale. Renewed sampling of the Alsace sites in 2001 showed that three populations had become extinct and significant genetic changes had occurred in the remaining four populations. The frequencies of extinction and colonization events at several spatial scales suggest a hierarchical metapopulation structure for M. tanacetaria. Frequent population turnover and drift are likely causes for the genetic differentiation of M. tanacetaria populations.

Animals↗
PubMed2006

The solution structure of stilbenoid dendrimers: a small-angle scattering study.

The spatial structure of a stilbenoid dendrimer is investigated by small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) in dilute solution. All measurements are performed in toluene. The dendrimer consists of a stilbenoid scaffold with appended hexyloxy chains. SAXS is mainly sensitive to the dendrimer scaffold whereas SANS intensity, measured in fully deuterated toluene, derives from the solute molecules. The resulting SAXS and SANS intensities are analyzed by comparison with various models. It is found that the model of a circular disk gives the best description of the data. SAXS data demonstrate that the stilbenoid scaffold is flat as expected for benzene rings conjugated through vinylene units. Thus, it can be described by a circular disk with a radius of 1.6 nm and a thickness of 0.7 nm. SANS, on the other hand, shows that the hexyloxy chains are not confined in the plane defined by the core. This is derived from modeling the SANS data with a much thicker circular disk (radius: 2.4 nm, thickness: 1.8 nm). The structure factor S(q), describing the interaction of the dendrimers at higher concentrations, is modeled quantitatively with the "polymer reference interaction site model" (PRISM) integral equation formalism for hard plates such as particles. Here the structural data obtained from the analysis of the SANS data are used so that no new adjustable parameter is necessary for this description.

Journal Article↗
PubMed2000

NMR structure of the channel-former zervamicin IIB in isotropic solvents.

Spatial structure of the membrane channel-forming hexadecapeptide, zervamicin IIB, was studied by NMR spectroscopy in mixed solvents of different polarity ranging from CDCl3/CD3OH (9:1, v/v) to CD3OH/H2O (1:1, v/v). The results show that in all solvents used the peptide has a very similar structure that is a bent amphiphilic helix with a mean backbone root mean square deviation (rmsd) value of ca. 0.3 A. Side chains of Trp1, Ile2, Gln3, Ile5 and Thr6 are mobile. The results are discussed in relation to the validity of the obtained structure to serve as a building block of zervamicin IIB ion channels.

Amino Acid Sequence↗
PubMed1999

Visual form created solely from temporal structure.

In several experiments, it was found that global perception of spatial form can arise exclusively from unpredictable but synchronized changes among local features. Within an array of nonoverlapping apertures, contours move in one of two directions, with direction reversing randomly over time. When contours within a region of the array reverse directions in synchrony, they stand out conspicuously from the rest of the array where direction reversals are unsynchronized. Clarity of spatial structure from synchronized change depends on the rate of motion reversal and on the proportion of elements reversing direction in synchrony. Evidently, human vision is sensitive to the rich temporal structure in these stochastic events.

Brain↗
PubMedDate not supplied

[Structure-functional organization of the secretin molecule. II. Direct conformation problem].

Spatial structure of peptide hormone secretin was investigated by the theoretical conformational method. A solution of the "direct conformational problem" for this hormone indicated that the possible structure of the secretin molecule under polar conditions may be described only by two families of low-energy conformations, possessing relatively conformational valid (Thr7-Leu22) and variable (His1-Phe6 and Leu23-Val27NH2) fragments. One of these families is comprised by five twists of the alpha-helix, while the second isoenergetic family possesses two short segments of the alpha-helix, divided by an irregular structure of the tetrapeptide.

Amino Acid Sequence↗