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PubMed1986

X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor.

Orthorhombic crystals diffracting beyond 1.7 A resolution, have been grown from the stoichiometric complex formed between human leukocyte elastase (HLE) and the third domain of turkey ovomucoid inhibitor (OMTKY3). The crystal and molecular structure has been determined with the multiple isomorphous replacement technique. The complex has been modeled using the known structure of OMTKY3 and partial sequence information for HLE, and has been refined. The current crystallographic R-value is 0.21 for reflections from 25 to 1.8 A resolution. HLE shows the characteristic polypeptide fold of trypsin-like serine proteinases and consists of 218 amino acid residues. However, several loop segments, mainly arranged around the substrate binding site, have unique conformations. The largest deviations from the other vertebrate proteinases of known spatial structure are around Cys168. The specificity pocket is constricted by Val190, Val216 and Asp226 to preferentially accommodate medium sized hydrophobic amino acids at P1. Seven residues of the OMTKY3-binding segment are in specific contact with HLE. This interaction and geometry around the reactive site are similar as observed in other complexes. It is the first serine proteinase glycoprotein analysed, having two sugar chains attached to Asn159 and to residue 109.

Animals↗

PubMed1995

Amino acid residue: is it structural or functional?

A new approach is suggested for delineating the structural and functional amino acid residues in proteins with known three-dimensional structure, basing on the involvement of residues in intramolecular hydrophobic and hydrophilic interactions and additional information about the conservativity of the residues. The approach is applied to the families of homologous neurotoxins and cardiotoxins. The results obtained concerning the role of amino acid residues in both families of toxins accord well with the similarity of their fold, but different mechanisms of action. Current approach can be used for detailed characterization of protein spatial structures, as well as for rational protein engineering.

Amino Acid Sequence↗

PubMed1993

Chaos and complexity in measles models: a comparative numerical study.

Recurrent epidemics of measles in developed countries offer a proving ground for current theories of complicated dynamics in ecological and epidemiological systems. This paper contrasts the basic forced SEIR model for measles with a variety of more complicated and realistic models, showing that variations in seasonal forcing and age-structured mixing patterns can generate a wide range of global dynamics. The well-known chaotic dynamics of the forced SEIR model appear to be absent from more realistic models, suppressed by the buffering effect of a low-risk group of pre-school children. These results, and the variety of measles dynamics seen in real populations with different demographic and geographic patterns, point out the need for age- and spatially-structured measles models and suggest caution in the construction of models for complicated systems.

Age Factors↗

PubMed2006

Conformational behavior of poly(L-lactide) studied by infrared spectroscopy.

This paper reports the analysis of the C=O stretching region of poly(L-lactide). This spectral band splits into up to four components, a phenomenon that a priori can be explained in terms of carbonyl-carbonyl coupling or specific interactions (such as C-H...O hydrogen bonding or dipole-dipole). Hydrogen bonding can be discarded from the analysis of the C-H stretching spectral region. In addition, low molecular weight dicarbonyl compounds of chemical structure similar to that of PLLA, such as diacyl peroxides, show a remarkable splitting of the carbonyl band attributed to intramolecular carbonyl-carbonyl coupling. Several mechanisms can be responsible for this behavior, such as mechanical coupling, electronic effects, or through-space intramolecular TDC (transition dipole coupling) interactions. Intermolecular dipole-dipole interactions (possible in the form of interchain TDC interactions) are proven to be of minor relevance taking into account the spatial structure of the PLLA conformers. The Simply Coupled Oscilator (SCO) model, which only accounts for mechanical coupling, has been found to predict adequately the relative intensity of the symmetric and asymmetric bands of dicarbonyl compounds. The dispersion curves predicted for PLLA by the SCO model also match those given by more general treatments, such as Miyazawa's first-order perturbation theory. Hence, the SCO model is adopted here as an adequate yet simple tool for the interpretation of band splitting caused by intramolecular coupling of polylactide. The four components observed in the C=O stretching band of semicrystalline PLLA are attributed to the four possible conformers: gt, gg, tt, and tg. The narrow bands observed for the interlamellar material are attributed to highly ordered chains, indicating the absence of a truly amorphous phase in the crystalline polymer. The interphase seems to extend over the whole interlamellar region, showing the features of a semiordered metastable phase. In amorphous PLLA, bands corresponding to gt, gg, and tt conformers also can be resolved by second derivative techniques, and curve-fitting results provide information about the conformational population at different temperatures.

Hydrogen Bonding↗

PubMed2002

Effect of diffusion and spatially varying predation risk on the dynamics and equilibrium density of a predator-prey system.

Starting from natural planktonic systems, we present a new mechanism involving spatial heterogeneity, and develop a new spatial structure model of planktonic predation systems. Firstly, the effect of diffusion on the dynamics of the system is investigated. We find that diffusion of only prey or both prey and predator between different patches with different predation risk may stabilize the dynamics, depending on the flow rate. Only a medium flow rate can lead to the stability of the system. Too large a rate can cause the system to approach the non-spatial limit case of a well-mixed system. Too large a rate can cause the system to approach the non-spatial limit case as a well-mixed system, which is characterized by its strongly oscillatory dynamics. When only prey diffuse, the smaller the parameter f (the proportion of the patchy volume with larger predation risk to the total volume), the more stable the system. If both populations can diffuse, however, only medium and very small f values may stabilize the system. Also, the response of the spatially averaged equilibrium densities of the system to the increasing of the flow rate is examined. With increasing flow rate, the spatial-averaged equilibrium density of prey decreases, while that of predator depends on which species can diffuse. For the case of prey diffusion only, it first remains unchanged and then slightly decreases, while it increases for the case of combinations as the flow rate increases. Our results are, qualitatively, determined by the spatially heterogeneous mechanism that we propose, and further regulated by top-down forces. Of practical importance, the results reported here indicate that which species diffuse plays a key role in the ways in which diffusion influences the dynamics and the spatial-average equilibrium densities of the system responses to the flow rate's increasing.

Animals↗

PubMed1986

Simulation of molecular dynamics of water movement in ion channels.

The motion of water molecules in a gramicidin-like channel was studied by the molecular dynamics method. Water molecules are presented in the ST2 model. The structure of the channel was presented in the form of channel's helix frame possessing mobile dipole groups. The interaction of all mobile particles with the membrane channel's walls was taken into account. The calculation consisted of 50,000 integration steps of delta t = 5 x 10(-16) s which corresponded to a total elapsed time of 25 ps. It was shown that water molecules in the channel did not possess rigid spatial structure but exhibited a structure oriented along the channel axis. The motion of water molecules in the channel occurred smoothly, i.e. all water molecules did not have any deep, stable potential wells in the channel. The distribution of water molecules along the radial coordinate of the channel was estimated. Water density was shown to be maximal near the channel axis.

Chemical Phenomena↗

PubMed2006

[Evaluation of maximum intensity projection in HRCT in the diagnosis of the destruction of ossicular chain in chronic otitis media].

OBJECTIVE: To observe the ossicular chain structure with maximum intensity projection (MIP) and to evaluate the diagnostic value of it in the destruction of ossicular chain in chronic otitis media (COM). METHOD: Sixty-eight patients (136 ears) were scanned with HRCT. The original data was processed with MIP reconstruction technique. The images of the ossicular chain structure in normal ears were observed, while the images in suffering ears were compared with the findings in operation. RESULT: In normal ears, the ossicular chain structure was shown clearly by MIP, which can also display three-dimensional images of the ossicular chain. In the suffering ears of chronic otitis media of cholesteatoma type, granuloma type and simple type, MIP displayed the destruction of ossicular chain in 39 ears, 5 ears and 0 ear respectively, which was observed in 39 ears, 6 ears and 0 ears respectively in operation. CONCLUSION: MIP technique in HRCT can display the ossicular chain spatial structure clearly, which is very helpful to evaluate the destruction of ossicular chain in chronic otitis media (COM) and to make accurate operation plan.

Adolescent↗

PubMed2001

A mathematical comparison of two models of the electrical properties of biological tissues.

The purpose of this paper is to compare two models of the electrical properties of tissue, which may be used to relate the effective conductivity to the volume fraction f of cells in the tissue. Both models assume that tissue comprises spherical cells, which behave electrically as dipoles. The first model, developed by Hanai, describes the tissue as a concentrated suspension of weakly conducting spheres in a conducting medium, with each sphere experiencing a uniform mean field. The second approach, developed by Chiew and Glandt, explicitly describes the effect of a random but statistically homogeneous cell structure on the average field and magnitude of the dipole interaction. The two analyses are identical to first order in f, but differ in the way in which the interactions between the dipoles are accounted for. The model developed by Chiew and Glandt appears to offer a more robust theoretical framework for describing the electrical properties of tissue. The comparison aims to contribute to an improved understanding of the relationship between the electrical properties and spatial structure of tissue.

Electric Conductivity↗

PubMed1997

Molecular divergence of lysozymes and alpha-lactalbumin.

The vast number of proteins that sustain the currently living organisms have been generated from a relatively small number of ancestral genes that has involved a variety of processes. Lysozyme is an ancient protein whose origin goes back an estimated 400 to 600 million years. This protein was originally a bacteriolytic defensive agent and has been adapted to serve a digestive function on at least two occasions, separated by nearly 40 million years. The origins of the related goose type and T4 phage lysozyme that are distinct from the more common C type are obscure. They share no discernable amino acid sequence identity and yet they possess common secondary and tertiary structures. Lysozyme C gene also gave rise, after gene duplication 300 to 400 million years ago, to a gene that currently codes for alpha-lactalbumin, a protein expressed only in the lactating mammary gland of all but a few species of mammals. It is required for the synthesis of lactose, the sugar secreted in milk. alpha-Lactalbumin shares only 40% identity in amino acid sequence with lysozyme C, but it has a closer spatial structure and gene organization. Although structurally similar, functionally they are quite distinct. Specific amino acid substitutions in alpha-lactalbumin account for the loss of the enzyme activity of lysozyme and the acquisition of the features necessary for its role in lactose synthesis. Evolutionary implications are as yet unclear but are being unraveled in many laboratories.

Amino Acid Sequence↗

PubMed2003

Investigation of the obscuring circumnuclear torus in the active galaxy Mrk231.

Active galaxies are characterized by prominent emission from their nuclei. In the 'unified' view of active galaxies, the accretion of material onto a massive compact object--now generally believed to be a black hole--provides the fundamental power source. Obscuring material along the line of sight can account for the observed differences in the nuclear emission, which determine the classification of AGN (for example, as Seyfert 1 or Seyfert 2 galaxies). Although the physical processes of accretion have been confirmed observationally, the structure and extent of the obscuring material have not been determined. Here we report observations of powerful hydroxyl (OH) line emissions that trace this obscuring material within the circumnuclear environment of the galaxy Markarian 231. The hydroxyl (mega)-maser emission shows the characteristics of a rotating, dusty, molecular torus (or thick disk) located between 30 and 100 pc from the central engine. We now have a clear view of the physical conditions, the kinematics and the spatial structure of this material on intermediate size scales, confirming the main tenets of unification models.

Journal Article↗

PubMedDate not supplied

4D bioinformatics: a new look at the ribosome as an example.

We have adapted the Java Molecular Viewer (JMV) to virtual reality display environments, through a number of extensions to the Java 3D code. Phylogenetic information derived from multiple alignments (temporal information) can be overlaid onto molecule structures (spatial information). The number of sequences included in the underlying multiple alignment can be changed instantaneously, resulting in dynamical updates of the displayed information. JMV was also extended to handle an infinite number of objects (molecules) in the same display. The objects can be manipulated in six degrees of freedom simultaneously or independently. We have used the small subunit ribosomal RNA to demonstrate the system (http:// cave.ucalgary.ca), which can be used for any molecule with a resolved structure.

Animals↗

PubMed2000

Electronic structure and nonlinear optical properties of model push-pull polyenes with modified indanone groups: a theoretical investigation

Several model polyenes with modified indanone groups were studied by means of density functional theory (DFT) B3LYP/6-31G*, ab initio HF/3-21G* and semiempirical AM1 methods. We investigated the effect of several substituents upon the relationship between the structure, spatial distribution of the highest occupied and the lowest unoccupied pi-MOs, a concept of the global softness and the global hardness as well as both linear and nonlinear polarizabilities for the set of pi-electron chromophores represented by the short-chain model polyene (butadiene) carrying out p-methoxyphenyl group on the one end and several modified indanone groups on the opposite end of the molecule. As probing endocyclic groups used to modify the structure of indanone the following substituents: > CH2; > C=O; > SO2, > C=CH(NO2) and > C=C(CN)2 were selected. The cubic relationship between the polarizability and the global softness was found. The highest polarizabilities (alpha, beta, gamma) are predicted for the derivatives with > C=C(CN)2 group. It was found that the value of beta depends mainly on the difference between dipole moments in the excited and ground states of the molecules. In the case of > SO2 group the results of AMI calculations significantly deviate from relationships found for other derivatives. Experimental IR and Raman spectra of newly synthesized indandione derivative of cinnamaldehyde were compared with computed ones.

Journal Article↗

PubMed1993

Lantibiotics--unusually modified bacteriocin-like peptides from gram-positive bacteria.

Lantibiotics are antibacterial peptides frequently produced by Gram-positive bacteria. They are distinguished by unique structural properties unprecedented so far in peptide chemistry. The most striking feature is the occurrence of intramolecular rings introduced by the thioether amino acids lanthionine and 3-methyllantionine. Additional usual amino acids such as didehydroalanine and didehydrobutyrine are found. Lantibiotics are produced from ribosomally synthesized prepeptides and the unusual amino acids are formed by post-translational modifications. This review summarizes the current knowledge on the biosynthetic mechanisms and enzymes taking part in biosynthesis, on the primary and spatial structures of the active peptides and the correlation between structural aspects and the antibacterial activity. Furthermore, the mode of action of type-A lantibiotics and the immunity phenomenon are described, and an outlook for future research and potential applications is given.

Alanine↗

PubMed2006

Modelling Southern Ocean ecosystems: krill, the food-web, and the impacts of harvesting.

The ecosystem approach to fisheries recognises the interdependence between harvested species and other ecosystem components. It aims to account for the propagation of the effects of harvesting through the food-web. The formulation and evaluation of ecosystem-based management strategies requires reliable models of ecosystem dynamics to predict these effects. The krill-based system in the Southern Ocean was the focus of some of the earliest models exploring such effects. It is also a suitable example for the development of models to support the ecosystem approach to fisheries because it has a relatively simple food-web structure and progress has been made in developing models of the key species and interactions, some of which has been motivated by the need to develop ecosystem-based management. Antarctic krill, Euphausia superba, is the main target species for the fishery and the main prey of many top predators. It is therefore critical to capture the processes affecting the dynamics and distribution of krill in ecosystem dynamics models. These processes include environmental influences on recruitment and the spatially variable influence of advection. Models must also capture the interactions between krill and its consumers, which are mediated by the spatial structure of the environment. Various models have explored predator-prey population dynamics with simplistic representations of these interactions, while others have focused on specific details of the interactions. There is now a pressing need to develop plausible and practical models of ecosystem dynamics that link processes occurring at these different scales. Many studies have highlighted uncertainties in our understanding of the system, which indicates future priorities in terms of both data collection and developing methods to evaluate the effects of these uncertainties on model predictions. We propose a modelling approach that focuses on harvested species and their monitored consumers and that evaluates model uncertainty by using alternative structures and functional forms in a Monte Carlo framework.

Animals↗

PubMed2003

Small scale velocity jumps in shear turbulence.

We measure structure functions and structures in uniformly sheared strong turbulence using an array of hot-wire velocity sensors. We find that the large-scale shear persists down to the smallest scales. There is a marked asymmetry between velocity increments measured in the shear direction, and those measured in the plane perpendicular to it. In the shear direction the scaling exponents tend to a constant, signifying the presence of small-scale cliffs. Direct evidence for those is presented by the spatial structure of the strongest velocity gradients.

Journal Article↗

PubMed2004

Fine-scale genetic structure of grape phylloxera from the roots and leaves of Vitis.

Patterns of variation at microsatellite loci suggest that root populations of the pest grape phylloxera (Daktulosphaira vitifoliae) are largely parthenogenetic in Australian vineyards. To investigate reproduction in leaf galling phylloxera and the association between these individuals and phylloxera on roots, we examined in detail genetic variation in phylloxera from a vineyard block. Some genotypes found on leaf galls within this block were not present on roots, whereas others spanned both zones. There was no evidence that genotypes on roots were the product of sexual reproduction in leaf galls. mtDNA variation was not associated with the location of the phylloxera clones. The spatial distribution of genotypes within a root population was further investigated by intensively sampling phylloxera from another vineyard block. Join-count spatial autocorrelation statistics were used to explore fine-scale spatial structure. Clones were nonrandomly distributed within the block and there was evidence that the distribution of clones followed rows. These findings suggest firstly that there is limited dispersal of root and leaf feeding phylloxera, and secondly that factors, other than vine host, are likely to be important and contribute to clonal structure within populations.

Animals↗

PubMed2004

Recurrent epidemics in small world networks.

The effect of spatial correlations on the spread of infectious diseases was investigated using a stochastic susceptible-infective-recovered (SIR) model on complex networks. It was found that in addition to the reduction of the effective transmission rate, through the screening of infectives, spatial correlations have another major effect through the enhancement of stochastic fluctuations, which may become considerably larger than in the homogeneously mixed stochastic model. As a consequence, in finite spatially structured populations significant differences from the solutions of deterministic models are to be expected, since sizes even larger than those found for homogeneously mixed stochastic models are required for the effects of fluctuations to be negligible. Furthermore, time series of the (unforced) model provide patterns of recurrent epidemics with slightly irregular periods and realistic amplitudes, suggesting that stochastic models together with complex networks of contacts may be sufficient to describe the long-term dynamics of some diseases. The spatial effects were analysed quantitatively by modelling measles and pertussis, using a susceptible-exposed-infective-recovered (SEIR) model. Both the period and the spatial coherence of the epidemic peaks of pertussis are well described by the unforced model for realistic values of the parameters.

Disease Outbreaks↗

PubMedDate not supplied

[Contribution of lectin sugar-binding peptides structure determines specificity of rhizobium-legume symbiosis in Galega orientalis and G. officinalis].

A significant heterogeneity between bacteria Rhizobium galegae bv. officinalis and R. galegae bv. orientalis forming the nitrogen-fixing symbiosis with Galega officinalis and G. orientalis, respectively, and not forming any single cross-inoculation group, was found by means of RAPD and RFEL methods. The high level of sequence similiraty between lectins of these plants indicates at their close relationship. However the sequences of lectin sugar binding peptides (SBP) of G. orientalis (TYCNPGWDPRDR) and G. officinalis (TFYNEEWDLVIKDEH) were highly diverged. Amino acids of SBP which are involved in linkage of Ca2+ and Mn2+ ions responsible for stabilization of spatial structure of carbohydrate-binding "pocket", keep their position in peptide. It suggests that lectins participate in Rhizobium-legume symbiosis and that carbohydrate-binding site plays a key role in this process.

Amino Acid Sequence↗