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PubMed2002

QSAR of HIV-1 integrase inhibitors by genetic function approximation method.

Quantitative structure--activity relationship (QSAR) paradigm, using genetic function approximation (GFA) technique was used to examine the correlations between the calculated physicochemical descriptors and the in vitro activities (3'-processing and 3'-strand transfer inhibition) of a series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors. Depending on the chemical structure, all molecules were divided into two classes---catechols and noncatechols. Eighty-one molecules were used in the present study and they were divided into training set and test set. The training set in each class consisted of 35 molecules and QSAR models were generated separately for both catechols and noncatechols. Equations were evaluated using internal as well as external test set predictions. Models generated for catechols show that electronic, shape related, and thermodynamic parameters are important whereas for noncatechols, spatial, structural, and thermodynamic properties play an important role for the activity.

Anti-HIV Agents↗

PubMed2003

Fine-scale genetic structure of two carabid species with contrasted levels of habitat specialization.

Using microsatellite markers, we compared the genetic structure of populations of two carabid species, one described as a generalist (commonly found in forest and in open habitats) and the other known as a forest specialist. Both species were sampled in the same forest plots, which were separated from each other by either open or forested areas. At the local scale considered (13.6 km separating the most distant plots), genetic differentiation was substantial for both species studied, but populations of the forest specialist Carabus punctatoauratus appeared to be more spatially structured than those of C. nemoralis. Isolation by distance analyses showed that nonforested areas are partial barriers to gene flow for both species studied, although more clearly for the forest specialist. Between and within forests, dispersal capacity of the generalist C. nemoralis was shown to be higher than that of the specialist C. punctatoauratus.

Animals↗

PubMed1996

Recognition of transmembrane alpha-helical segments with environmental profiles.

A method for assessing the environmental properties of membrane-spanning alpha-helical peptides in proteins has been proposed. The algorithm employs a set of environmental preference parameters derived for amino acid residues based on the analysis of the 3-D structures of membrane domains in bacteriorhodopsin and photoreaction centers Rhodopseudomonas viridis and Rhodobacter sphaeroides. The resulting 3-D-1-D scores for transmembrane segments are significantly different from those derived for alpha-helices in globular proteins. The parameters obtained have been used to construct environmental profiles for membrane alpha-helices in bacteriorhodopsin and photoreaction centers. The profiles successfully recognize their own sequences in several specially designed large databases. The method has been applied to several membrane proteins with unknown spatial structures. Most of their membrane-spanning peptides were efficiently recognized by the profiles. The predicted environment of the residues in the membrane segments fits the experimental data well. The approach is independent of any homology data and can be employed to delineate the membrane segments of a protein with environmental characteristics close to those of bacteriorhodopsin and photoreaction centers. The alignment of these segments with the reference profiles provides a considerable amount of data about their lipid and protein exposure.

Algorithms↗

PubMed2003

[The Nobel Prize in Chemistry 2003 awarded for discoveries concerning molecular channels in cell membranes].

About 70% of the human body consists of salt water. The Nobel Prize 2003 in Chemistry rewards Peter Agre for the discovery of water channels and Roderick MacKinnon for structural and mechanistic studies of ion channels. Their studies have demonstrated how ions and water are transported through cell membranes. This transport is essential for the regulation of size and osmotic pressure in cells and organelles and it plays a major role in salt and water homoeostasis and in the generation of electrical signals in nerve cells. Agre succeeded in isolating a membrane protein which later studies revealed to be a long-postulated water channel, MacKinnon succeeded in determining the spatial structure of a potassium channel.

Aquaporins↗

PubMedDate not supplied

[Structure-activity analysis of ribonuclease A and related proteins].

A detailed analysis of noncovalent interactions in the RNase A molecule was carried out. For this purpose, contact maps based on structural data were constructed. Three hydrophobic nuclei and five microclusters were identified, and their quantitative parameters were calculated. The contacts between amino acid residues of the active center and the hydrophobic nuclei were established. The distribution of the charged amino acid residues on the of RNase A surface was shown. The data obtained was discussed in the context of the ribonuclease A family. The substitutions seen from the alignment of amino acid sequences in the family might have influence on the spatial structure of different parts of RNase A and their mutual orientation and, consequently on the biological activity of family members.

Amino Acid Sequence↗

PubMed2006

Dynamical behavior of hydrodynamic Lyapunov modes in coupled map lattices.

In our previous study of hydrodynamic Lyapunov modes (HLMs) in coupled map lattices, we found that there are two classes of systems with different lambda-k dispersion relations. For coupled circle maps we found the quadratic dispersion relations lambda approximately k2 and lambda approximately k for coupled standard maps. Here, we carry out further numerical experiments to investigate the dynamic Lyapunov vector (LV) structure factor which can provide additional information on the Lyapunov vector dynamics. The dynamic LV structure factor of coupled circle maps is found to have a single peak at omega=0 and can be well approximated by a single Lorentzian curve. This implies that the hydrodynamic Lyapunov modes in coupled circle maps are nonpropagating and show only diffusive motion. In contrast, the dynamic LV structure factor of coupled standard maps possesses two visible sharp peaks located symmetrically at +/- omega. The spectrum can be well approximated by the superposition of three Lorentzian curves centered at omega=0 and +/-omegau, respectively. In addition, the omega-k dispersion relation takes the form omegau=cuk for k --> 2pi/L. These facts suggest that the hydrodynamic Lyapunov modes in coupled standard maps are propagating. The HLMs in the two classes of systems are shown to have different dynamical behavior besides their difference in spatial structure. Moreover, our simulations demonstrate that adding damping to coupled standard maps turns the propagating modes into diffusive ones alongside a change of the lambda-k dispersion relation from lambda approximately k to lambda approximately k2. In cases of weak damping, there is a crossover in the dynamic LV structure factors; i.e., the spectra with smaller k are akin to those of coupled circle maps while the spectra with larger k are similar to those of coupled standard maps.

Journal Article↗

PubMed2001

The role of spike timing in the coding of stimulus location in rat somatosensory cortex.

Although the timing of single spikes is known to code for time-varying features of a sensory stimulus, it remains unclear whether time is also exploited in the neuronal coding of the spatial structure of the environment, where nontemporal stimulus features are fundamental. This report demonstrates that, in the whisker representation of rat cortex, precise spike timing of single neurons increases the information transmitted about stimulus location by 44%, compared to that transmitted only by the total number of spikes. Crucial to this code is the timing of the first spike after whisker movement. Complex, single neuron spike patterns play a smaller, synergistic role. Timing permits very few spikes to transmit high quantities of information about a behaviorally significant, spatial stimulus.

Action Potentials↗

PubMed2001

Exponential distance statistics to detect the effects of population subdivision.

Statistical tests are needed to determine whether spatial structure has had a significant effect on the genetic differentiation of subpopulations. Here we introduce a new family of statistics based on a sum of an exponential function of the distances between individuals, which can be used with any genetic distance (e.g., nucleotide differences, number of nonshared alleles, or separation on a phylogenetic tree). The power of the tests to detect genetic differentiation in Wright-Fisher island models and stepping stone models was calculated for various sample sizes, rates of migration and mutation, and definitions of spatial neighborhoods. We found that our new test was in some cases more powerful than the Ks* statistic of Hudson et al. (Mol. Biol. Evol. 9, 138-151, 1992), but in all cases was slightly less powerful than both a traditional chi2 test without lumping of rare haplotypes and the S(nn) test of Hudson (Genetics 155, 2011-2014, 2000). However, when we applied our new tests to three data sets, we found in some cases highly significant results that were missed by the other tests.

Animals↗

PubMedDate not supplied

[A non-statistical approach to the prediction of regular structures in proteins by the example of alpha-helices].

A new approach to the analysis of regular structures in proteins that is based on the method of molecular mechanics is proposed. The method uses only the information about the amino acid sequence. The alpha-helical conformation was simulated using the ICM program of molecular mechanics. Energy profiles of the sequences in the alpha-helical conformation, spanning the entire polypeptide chain, were plotted for eight proteins from the Protein Data Bank. The regions of each profile that exhibit energy minima were found to correspond to the alpha-helical regions of the real spatial structure of the protein. Twenty-four out of 25 helices were distinctly pronounced, which indicates a rather high accuracy of the prediction. The energy profiles also help reveal the short regions that correspond to 3/10-helices and the turns that include local alpha-helical conformations. Unlike the known statistical methods of prediction, this method makes it possible to establish the physical principles of the formation of alpha-helical conformations. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 6; see also http://www.maik.ru.

Energy Transfer↗

PubMed1991

Fluorescence study of the conformational properties of myoglobin structure. 2. pH- and ligand-induced conformational changes in ferric- and ferrousmyoglobins.

Tryptophanyl fluorescence of high-spin and low-spin complexes of sperm whale ferric- and ferrousmyoglobins, met-, azide- and cyanomyoglobins and deoxy-, oxy- and carboxymyoglobins has been studied in the pH range 2.5-13. The pH-dependent fluorescence of sperm whale metmyoglobin acylated at the N-terminal alpha-amino group by methylisothiocyanate and of bovine metmyoglobin, which contains invariant Trp7 and Trp14 but lacks Tyr151, have also been examined. Drastic changes in the fluorescence were registered in the acidic and alkaline pH ranges which are due to denaturation of Mb. Fluorescent and CD data indicate that at pH less than 4.5 and pH greater than 11.5 the unique spatial structure of the protein is destroyed whereas the secondary structure and integrity are essentially preserved. In all sperm whale and bovine myoglobins studied a local conformational change in the surroundings of Trp is observed which precedes alkaline denaturation. It seems to be due to deprotonation of lysine residues and breakage of the salt bridges essential for the maintenance of the native conformation of the N-terminal and the adjacent region. The parameters of this conformational transition are found to correlate with the spin state of the heme complex. However, analysis of the fluorescence behaviour of different ligand derivatives of myoglobin in the whole pH range studied enables one to conclude that the exact protein conformation depends not only on the spin state of the Fe atom but, to a greater extent, probably on the chemical nature of the ligand and its interaction with the protein groups in the heme cavity. Local conformational changes induced by the replacement of the sixth ligand or by varying pH seem to involve the same region of contacts between the A helix and GH fragment (or between the AE and GH helical complexes) though the extent of the changes may be different.

Animals↗

PubMed1984

Centripetal myosin redistribution in thrombin-stimulated platelets. Relationship to platelet Factor 4 secretion.

We have examined the F-actin and myosin distribution in resting and thrombin-activated platelets by double label immunofluorescence microscopy. In resting, discoid platelets, F-actin and myosin staining was distributed in a diffuse pattern throughout the interior of the cell with slight accentuation at the cell periphery. In contrast, platelet factor 4 antigen (PF4) was more centrally localized in a fine punctate distribution which is consistent with its localization in alpha-granules. Within 5 sec after thrombin stimulation both F-actin and myosin staining were increased at the periphery of the now spherical platelets. Subsequently, a myosin-containing spherical structure decreased in diameter closely surrounding a phase-dense central zone. In contrast, F-actin staining continued to be accentuated at the cell periphery and was prominent in filopodia and blebs. As previously shown, PF4 staining was localized after 30 sec within large intracellular masses that corresponded to closed vacuolar structures at the ultrastructural level. Morphometric analysis of electron micrographs showed that formation of these vacuolar structures kinetically paralleled alpha-granule disappearance and preceded PF4 release. These PF4-containing structures translocated to the cell periphery after 1-3 min, where they appeared to fuse with the plasma membrane. Ultrastructural analysis of thin sections showed that the myosin-rich spherical structure spatially and temporally correlated with a band of microfilaments that closely surrounded the organelle-rich central zone of the cell. Morphometric analysis of these micrographs showed that the absolute volume of this central zone decreased with time after thrombin addition, showing a significant change after 15 sec and reaching a maximum value after 3-5 min. Changes in the volume of this compartment kinetically preceded PF4 release. On the basis of these data, we propose that an actomyosin contractile force is generated which centripetally redistributes the myosinrich structure and organelle zone. Conceivably this inward force may not only accelerate granule-granule fusion to form intracellular secretory vacuoles, but may also provide aid in their extrusion toward the platelet plasma membrane.

Actins↗

PubMed1994

Insights into the different exploits of colour in the visual cortex.

A new method that allows controlled masking of luminance contrast has been developed to study the use of chromatic signals in human vision. The method also makes it possible to examine the different uses of chromatic signals (e.g. the generation of perceived colour, or the construction and representation of object structure and form). By using this technique, we studied the threshold detection of chromatic signals in normal trichromats. The results show that chromatic signals are virtually unaffected by ongoing, randomly varying, luminance contrast changes. These findings suggest that chromatic signals are either processed independently or can be separated completely from any confounding luminance contrast components in the stimulus. Thresholds for detection of colour changes only, and for extraction of stimulus structure from chromatic signals in normal trichromats, in subjects with single cone receptor deficiency (i.e. dichromats) and in three subjects with abnormal colour vision caused by bilateral damage to ventromedial, extra-striate visual cortex (i.e. subjects with cerebral achromatopsia) have also been measured. No significant difference in thresholds for the two conditions was observed either in normal trichromats or in dichromats. Subjects with cerebral achromatopsia, however, reveal markedly different thresholds. The results suggest that chromatic signals are processed independently to generate perceived object colour or to construct spatially structured objects, and that these functions involve different neural substrates. The results help to explain, at least in part, why cerebral achromatopsia is a heterogeneous disorder, and why there can be significant differences in the effective use of chromatic signals in subjects described as cerebral achromatopsics.

Color Perception↗

PubMed1979

Structural characterization by nuclear magnetic resonance of a reactive-site 13carbon-labelled basic pancreatic trypsin inhibitor with the peptide bond Arg-39--Ala-40 cleaved and Arg-39 removed.

With the use of an enzymatic replacement method, 90%-enriched [1-13C]lysine was introduced into the reactive site of the basic pancreatic trypsin inhibitor. Characterization of the labelled inhibitor with 13C nuclear magnetic resonance (NMR), 1H NMR and chemical methods showed that while the reactive-site peptide bond Lys-15--Ala-16 was properly resynthesized, the polypeptide chain was cleaved at the peptide bond Arg-39--Ala-40 and Arg-39 was removed. Detailed 1H NMR studies showed further that, with the exception of the immediate environment of the modification site, the average spatial structure of the native inhibitor was preserved in the modified protein. Compared to the native inhibitor, the thermal stability of the globular conformation was found to be reduced, interior amide protons exchanged at a faster rate and the internal mobility of aromatic rings located outside the immediate environment of the cleaved peptide bond was essentially unchanged. These observations coincide closely with previous reports on different modifications of the inhibitor and can be explained by a recently proposed dynamic multi-state model for globular proteins. Since the fundamental structural properties of the native inhibitor and full inhibitory activity are preserved after resynthesis, the [1-13C]lys-15-labelled inhibitor with the peptide bond Arg-39--Ala-40 cleaved and Arg-39 removed should be suitable for 13C NMR studies of mechanistic aspects of proteinase-inhibitor interactions.

Alanine↗

PubMed1984

Conformational changes in the globin family during evolution. 1. Analysis of the evolutionary role of insertions and deletions.

Conformational restrictions imposed on the fixation of insertions and deletions by the three-dimensional structure of globins during evolution are analyzed. An evolutionary tree for the primary structure of 38 taxonomically distant globins was constructed by a computer method. Based on this tree, the calculated fixation frequency of point mutations was 50-fold higher than that established jointly for deletions and insertions, and the fixation frequency of deletions was more than three times that established for insertions. It was also found that deletions and insertions are predominantly fixed in the interhelical sections and at the ends of the alpha-helices of the globin molecules. Conformational analysis of the packing of the alpha-helices in the spatial structure of globins demonstrated that the fixation of deletions and insertions in the center of an alpha-helix produces a marked distortion of their normal packing. The possible role of deletions and insertions in the evolution of protein families is discussed.

Animals↗

PubMed2005

Spatial self-organization in a cyclic resource-species model.

Biological communities are remarkable in their ability to form cooperative ensembles that lead to coexistence through various types of niche partitioning, usually intimately tied to spatial structure. This is especially true in microbial settings where differential expression and regulation of genes allows members of a given species to alter their lifestyle so as to fill a functional role within the community. The resulting species interactions can involve feedback, as in the case of some bacterial consortia that participate in the cooperative degradation of a given resource in a succession of steps and in such a way that certain "later" species provide catalytic support for the primary degrader. We seek to capture the essential features of such spatially extended biological systems by introducing a lattice-based stochastic spatial model (interacting particle system) with cyclic local dynamics. Here, a given site progresses through a sequence of resource and species states in a prescribed order. Furthermore, this succession of states (at a site) is assumed to form a cyclic pattern due to a natural feedback mechanism. We explore conditions under which all the species are able to coexist and consider the extent to which this coexistence requires the development of spatio-temporal patterns, including spiral waves. This self-organization, if it occurs, results when synchronization of the dynamics at the microscopic level leads to macroscopic patterns. These patterns result in consumer-driven resource fluctuations that generate a form of spatio-temporal niche partitioning. As with most models of this complexity, we employ a mixture of mathematical analysis and simulations to develop an understanding of the resulting dynamics.

Adaptation, Biological↗

PubMedDate not supplied

Reconstruction and visualization of planetary nebulae.

From our terrestrially confined viewpoint, the actual three-dimensional shape of distant astronomical objects is, in general, very challenging to determine. For one class of astronomical objects, however, spatial structure can be recovered from conventional 2D images alone. So-called planetary nebulae (PNe) exhibit pronounced symmetry characteristics that come about due to fundamental physical processes. Making use of this symmetry constraint, we present a technique to automatically recover the axisymmetric structure of many planetary nebulae from photographs. With GPU-based volume rendering driving a nonlinear optimization, we estimate the nebula's local emission density as a function of its radial and axial coordinates and we recover the orientation of the nebula relative to Earth. The optimization refines the nebula model and its orientation by minimizing the differences between the rendered image and the original astronomical image. The resulting model allows creating realistic 3D visualizations of these nebulae, for example, for planetarium shows and other educational purposes. In addition, the recovered spatial distribution of the emissive gas can help astrophysicists gain deeper insight into the formation processes of planetary nebulae.

Algorithms↗

PubMed2006

Chemical shift anisotropic mapping of a coherent optical absorber using magnetic field induced quantum beats.

A new method for mapping the spatial structure of optical coherent materials which relies on imposing a set of linear orthogonal gradient magnetic fields for a controlled hyperfine splitting of energy levels to create characteristic quantum beats when illuminated with a laser pulse with sufficient bandwidth to excite these levels is proposed. In this approach, a spectroscopic fingerprint of the dopant sites due to concentration and field susceptibilities in the sample is achieved through a Fourier decomposition of the radiative relaxation decay in an approach analogous to nuclear magnetic resonance spectroscopy due to the imposition of a controlled spatial-spectral encoding scheme. A three pulse sequence necessary to interrogate a gradient resolved voxel is also discussed. This three pulse approach can be combined with the conventional confocal imaging technique to provide information about the underlying chemistry of dopant distribution along each imaging plane which is useful in guiding the design and manufacturing process of optical crystals. In combination with gradient induced quantum beats, the entire inhomogeneous bandwidth can be interrogated. The proposed approach would scan this entire bandwidth at much faster rate enabling characterization of a large number of crystals than is currently possible through mechanical scanning with a confocal microscopy based spectroscopic technique as well as providing functional dopant profiling which is not currently possible with conventional approaches.

Journal Article↗

PubMed1997

Band-limited contrast in natural images explains the detectability of changes in the amplitude spectra.

The psychophysical task of discriminating changes in the slopes of the amplitude spectra of complex images has been used in the past to test whether the human visual system might be optimised for coding the spatial structure in natural images (e.g. Knill et al., 1990; Tadmor & Tolhurst, 1994). We have reported that the dependency of these discrimination thresholds on the reference slope has the same overall general form, regardless of the particular digitised photographs that are used for generating the stimuli. The actual discrimination thresholds, however, differ markedly in magnitude for stimuli that are derived from different digitised photographs. Here, we describe a model that aims at explaining this diversity of threshold magnitudes: we suppose that the observer is detecting small changes in image contrast estimated within limited spatial-frequency bands of about 1 octave bandwidth. This local-contrast analysis reveals that contrast changes in only one frequency band are of comparable magnitudes to the changes that observers need for detecting differences in the Michelson contrast of simple sinusoidal gratings. The success of this band-limited contrast model is further shown in experiments where the slopes of the amplitude spectra of stimuli were changed only within restricted frequency bands. We show that when the slope is changed outside the limited frequency band implicated by the contrast model, the observer's thresholds are greatly elevated. Thresholds remain unchanged when slope changes are made within the implicated band. We also find that the exact bandwidth of the contrast operator is not critical, provided that it is in the range of about 0.6-1.5, which is the characteristic bandwidth range of V1 neurons.

Contrast Sensitivity↗