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At least 1,135 records · Page 63Linked to original sources
PubMed2006

Statistics of knots, geometry of conformations, and evolution of proteins.

Like shoelaces, the backbones of proteins may get entangled and form knots. However, only a few knots in native proteins have been identified so far. To more quantitatively assess the rarity of knots in proteins, we make an explicit comparison between the knotting probabilities in native proteins and in random compact loops. We identify knots in proteins statistically, applying the mathematics of knot invariants to the loops obtained by complementing the protein backbone with an ensemble of random closures, and assigning a certain knot type to a given protein if and only if this knot dominates the closure statistics (which tells us that the knot is determined by the protein and not by a particular method of closure). We also examine the local fractal or geometrical properties of proteins via computational measurements of the end-to-end distance and the degree of interpenetration of its subchains. Although we did identify some rather complex knots, we show that native conformations of proteins have statistically fewer knots than random compact loops, and that the local geometrical properties, such as the crumpled character of the conformations at a certain range of scales, are consistent with the rarity of knots. From these, we may conclude that the known "protein universe" (set of native conformations) avoids knots. However, the precise reason for this is unknown--for instance, if knots were removed by evolution due to their unfavorable effect on protein folding or function or due to some other unidentified property of protein evolution.

Evolution, Molecular↗
PubMedDate not supplied

[Irradiation by electrons of tubulin solution in vitro causes tubulin assembly in absence of a magnesium cofactor].

It was shown that irradiation of a tubulin solution (5 x 10(-6) mol/l) with electrons makes tubulin assemble to microtubules. The response of the system was monitored by the femtosecond laser technique. The assembly under these conditions occurs without Mg2+ (magnesium cofactor) and GTP. At 730 (the first harmonic) and 365 nm (the second harmonic), a rise in signal intensity occurs during the first 60-70 ns followed by the onset of tubulin assembly to microtubules, which was registered by the methods of spectrophotometry and electron spectroscopy. Theoretically this effect can be explained by the appearance of hydrated electrons in the solvated tubulin shell. Hydrated electrons are mostly in a long-living polaron state, which can be considered as an ensemble of quasi-dipoles of the electron-H3O+ type. The interaction of quasi-dipoles with the weak internal electrostatic field of tubulin leads, due to nonlinear effects, to a manifold rise in the intensity of the electrostatic field of the solvated shell of initially nonpolymerized tubulin chains. Finally, the increased field makes separate tubulin chains aggregate to microtubules. The effect observed is identical to the action of Mg2+ on the GTP site of beta-tubulin, which transfers it to a slightly perturbed triplet state.

Algorithms↗
PubMed1983

[Spatial organization of tissue elements of the caudate nucleus in the dog].

Simple methods for quantitative analysis of nerve cells and their processes in n. caudatus of dog are suggested. Some principal features of the internal arrangement of n. caudatus are established and correlated with other brain system. Graphic reconstruction of small cells ensembles and their distribution within the nucleus is given. Physiological role of small cell ensembles and large caudate cells (long axoned and short axoned) for caudatocortical transmission of excitation is considered.

Animals↗
PubMed1991

Long-term optical recording of patterns of electrical activity in ensembles of cultured Aplysia neurons.

1. Left upper quadrant (LUQ) cells isolated from the abdominal ganglion of Aplysia were maintained in culture to study how the cellular and synaptic properties of individual neurons contribute to the generation of patterns of electrical activity by neuronal ensembles. 2. Conventional microelectrodes were used to examine the spiking characteristics of individually cultured LUQ cells in vitro and to characterize their synaptic interactions. 3. In vitro, in contrast to in situ, LUQ neurons innervate other LUQ neurons. Intracellular recordings from pairs of LUQ cells showed that the prevalent type of postsynaptic potential was purely inhibitory. The other type of response was a dual-action postsynaptic potential, with inhibition followed by a delayed, slow excitation. 4. We established a set of criteria for the use of multiple-site optical recording techniques, in combination with impermeant probes of membrane potential, to observe the patterns of electrical activity generated by ensembles of co-cultured LUQ cells. 5. The spiking activity of individual cells within the neuronal ensembles was detected by means of the change in optical absorption of cells that were vitally stained with the dye RH155. The change in absorption was typically delta A congruent to 4 X 10(-4) per spike. We achieved a signal-to-noise (peak-to-peak) ratio of approximately 10 for a 50 X 50-microns photodetector field and an incident intensity of approximately 10 mW/cm2, close to the theoretical limit. 6. These conditions permitted, for the first time, continuous optical recording from cultured neurons for periods of up to 3 h with no discernible photodynamic damage or photobleaching. This long-term optical recording permitted examination of the different patterns of electrical activity generated by individual neuronal ensembles under several different experimental conditions. 7. An elaborate tracery of regenerated neurites present in these cultures resulted in individual photodetectors recording simultaneously the activity of multiple neurons. We reconstructed the temporal firing patterns for individual neurons within ensembles even with all the neurons active simultaneously and determined the functional connections in the ensemble by analyzing the temporal relationships between firing patterns of individual neurons. Excitatory as well as inhibitory functional interactions could be observed within the neuronal ensemble, the latter after the tonic activity of the neurons was increased by reducing the extracellular [Mg2+]. 8. Examination of the optical data from ensembles constructed from identified cells having characteristic physiological responses allowed us to address the question of how cellular and synaptic properties affect the patterns of electrical activity generated by neuronal ensembles.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1999

Conformational analysis of a novel cyclic enkephalin analogue using NMR and EDMC calculations.

Conformational space of a novel cyclic enkephalin analogue, cyclo(N(epsilon),N(epsilon')-carbonyl-D-Lys2,Lys5)enkephalin amide, was exhaustively examined. A large number of conformations was selected and clustered into families on the basis of their structure and energy. For representative conformations ROESY spectra were generated and their linear combination was fitted to the spectra measured in water and Me2SO-d6. This procedure yielded an ensemble of most populated conformations of the peptide in the two solvents.

Amides↗
PubMed2001

Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.

Solvation effects play a profound role in the energetics of protein folding. While a continuum dielectric model of solvation may provide a sufficiently accurate estimate of the solvation effects, until now this model was too computationally expensive and unstable for folding simulations. Here we proposed a fast yet accurate and robust implementation of the boundary element solution of the Poisson equation, the REBEL algorithm. Using our earlier double-energy scheme, we included for the first time the mathematically rigorous continuous REBEL solvation term in our Biased Probability Monte Carlo (BPMC) simulations of the peptide folding. The free energy of a 23-residue beta beta alpha-peptide was then globally optimized with and without the solvation electrostatics contribution. An ensemble of beta beta alpha conformations was found at and near the global minimum of the energy function with the REBEL electrostatic solvation term. Much poorer correspondence to the native solution structure was found in the "control" simulations with a traditional method to account for solvation via a distance-dependent dielectric constant. Each simulation took less than 40 h (21 h without electrostatic solvation calculation) on a single Alpha 677 MHz CPU and involved more than 40,000 solvation energy evaluations. This work demonstrates for the first time that such a simulation can be performed in a realistic time frame. The proposed procedure may eliminate the energy evaluation accuracy bottleneck in folding simulations.

Algorithms↗
PubMed1989

Use of a new strategy to isolate and characterize 436 Drosophila cDNA clones corresponding to RNAs detected in adult heads but not in early embryos.

We describe a new strategy for producing tissue-specific cDNA libraries and subsequently identifying tissue-specific clones. This method was used to screen for cDNA clones corresponding to RNAs expressed in the Drosophila head that cannot be detected in the early embryo. RNA blots were used to assess the spatial and temporal patterns of expression of these RNAs. The ensemble of 436 head-not-embryo clones identified roughly 700 distinct RNAs that are differentially expressed in the Drosophila head. The RNA expression patterns can be classified into five major categories. it is argued that this ensemble of clones represents a large fraction of all genes differentially expressed in the adult head, but not detected in the early embryo. Many of these genes are likely to encode eye- and nervous system-specific products.

Aging↗
PubMed2003

New theoretical expressions for the five adsorption type isotherms classified by BET based on statistical physics treatment.

New theoretical expressions to model the five adsorption isotherm types have been established. Using the grand canonical ensemble in statistical physics, we give an analytical expression to each of five physical adsorption isotherm types classified by Brunauer, Emett, and Teller, often called BET isotherms. The establishment of these expressions is based on statistical physics and theoretical considerations. This method allowed estimation of all the mathematical parameters in the models. The physicochemical parameters intervening in the adsorption process that the models present could be deduced directly from the experimental adsorption isotherms by numerical simulation. We determine the adequate model for each type of isotherm, which fixes by direct numerical simulation the monolayer, multilayer, or condensation character. New equations are discussed and results obtained are verified for experimental data from the literature. The new theoretical expressions that we have proposed, based on statistical physics treatment, are rather powerful to better understand and interpret the various five physical adsorption type isotherms at a microscopic level.

Journal Article↗
PubMed2003

Stiff polymer in monomer ensemble.

We employ an ordered monomer ensemble formalism in order to develop techniques to investigate a stiff polymer chain which is confined to a certain region. In particular, we calculate the segment density for a given location and segment orientation distribution within the confining geometry. With this method the role of the stiffness can be examined by means of differential equations, integral equations, or recursive relations for both continuum and lattice models. A suitable choice of lattice model permits an exact analytical solution for the segment location and orientation density for a chain between two parallel plates. For the stiff polymer in a spherical cavity we develop an integral equation formalism which is treated numerically, and in the same spherical geometry, a different model of the polymer displays a solution of a differential equation.

Journal Article↗
PubMed2001

Free energy self-averaging in protein-sized random heteropolymers.

Current theories of heteropolymers are inherently macroscopic, but are applied to mesoscopic proteins. To compute the free energy over sequences, one assumes self-averaging--a property established only in the macroscopic limit. By enumerating the states and energies of compact 18, 27, and 36mers on a lattice with an ensemble of random sequences, we test the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is valid at the scale of real proteins. The results validate sequence design methods which exponentially speed up computational design and simplify experimental realizations.

Models, Chemical↗
PubMed2000

Large-scale failures of f(-alpha) scaling in natural image spectra.

Several studies have demonstrated that the power spectra of natural image ensembles scale as f(-alpha). A stronger claim that has been made is that the power spectra of single natural images typically also scale as f(-alpha). Results are presented that challenge this latter claim. The results are based on a method for estimating large-scale structure in single images that compares aliasing artifacts produced by image windows of different shape. Failures of f(-alpha) scaling are found at large scales in many natural images. These failures cannot be accounted for by f(-alpha) scaling models such as a linear superposition model or a model based on two-dimensional occlusions in the image plane. The results imply that claims about f(-alpha) scaling in single natural images have been exaggerated. The results also offer insight into why such failures of f(-alpha) scaling occur.

Animals↗
PubMed2005

Fluorescence quenching by TEMPO: a sub-30 A single-molecule ruler.

A series of DNA molecules labeled with 5-carboxytetramethylrhodamine (5-TAMRA) and the small nitroxide radical TEMPO were synthesized and tested to investigate whether the intramolecular quenching efficiency can be used to measure short intramolecular distances in small ensemble and single-molecule experiments. In combination with distance calculations using molecular mechanics modeling, the experimental results from steady-state ensemble fluorescence and fluorescence correlation spectroscopy measurements both show an exponential decrease in the quenching rate constant with the dye-quencher distance in the 10-30 A range. The results demonstrate that TEMPO-5-TAMRA fluorescence quenching is a promising method to measure short distance changes within single biomolecules.

Base Sequence↗
PubMed1999

[Genetic algorithms in 3D-QSAR: The use of multiple ligand orientations for improved predictions of toxicity]

In a recent article in this journal, we discussed the application of a 3D-QSAR technique to the prediction of the toxicity of dibenzodioxins, dibenzofurans, and biphenyls (Vedani et al., 1999a). The use of such methods is legitimate because there is strong evidence that the toxicity is mediated by the Aryl hydrocarbon (Ah) receptor, a regulatory element involved in the mammalian metabolism of xenobiotics. In an extention to a concept developed at our laboratory (Vedani et al., 1998), we now show that safer predictions are possible if instead of a single - and, therefore, necessarily biased - assumption about the mutual orientation of the toxins, an ensemble of possible orientations is used for model construction. The contribution of a single entity within this ensemble to the toxin-receptor interaction energy is determined by a Boltzmann criterion. While in the single-orientation model two of the 26 toxins of an external test set were predicted false positive or false negative, all test substances are correctly predicted in the multiple-orientation model - including up to four different orientations per molecule - within a factor 10 of the experimental binding affinity. These results demonstrate that 3D-QSAR techniques based on a genetic algorithm can be used to predict the toxicity of chemical and pharmacological substances "in computo" if a receptor-mediated mechanism can be assumed. Consequently, the method can be used in toxicological screening assays, thereby replacing stressful tests on animals.

Journal Article↗
PubMed2006

Sensitivity of ecological models to their climate drivers: statistical ensembles for forcing.

Global and regional numerical models for terrestrial ecosystem dynamics require fine spatial resolution and temporally complete historical climate fields as input variables. However, because climate observations are unevenly spaced and have incomplete records, such fields need to be estimated. In addition, uncertainty in these fields associated with their estimation are rarely assessed. Ecological models are usually driven with a geostatistical model's mean estimate (kriging) of these fields without accounting for this uncertainty, much less evaluating such errors in terms of their propagation in ecological simulations. We introduce a Bayesian statistical framework to model climate observations to create spatially uniform and temporally complete fields, taking into account correlation in time and space, spatial heterogeneity, lack of normality, and uncertainty about all these factors. A key benefit of the Bayesian model is that it generates uncertainty measures for the generated fields. To demonstrate this method, we reconstruct historical monthly precipitation fields (a driver for ecological models) on a fine resolution grid for a climatically heterogeneous region in the western United States. The main goal of this work is to evaluate the sensitivity of ecological models to the uncertainty associated with prediction of their climate drivers. To assess their numerical sensitivity to predicted input variables, we generate a set of ecological model simulations run using an ensemble of different versions of the reconstructed fields. We construct such an ensemble by sampling from the posterior predictive distribution of the climate field. We demonstrate that the estimated prediction error of the climate field can be very high. We evaluate the importance of such errors in ecological model experiments using an ensemble of historical precipitation time series in simulations of grassland biogeochemical dynamics with an ecological numerical model, Century. We show how uncertainty in predicted precipitation fields is propagated into ecological model results and that this propagation had different modes. Depending on output variable, the response of model dynamics to uncertainty in inputs ranged from uncertainty in outputs that matched that of inputs to those that were muted or that were biased, as well as uncertainty that was persistent in time after input errors dropped.

Animals↗
PubMed1984

Dynamic light scattering study of muscle F-actin.

By use of digital autocorrelation and fast Fourier methods, dynamic light-scattering studies of in vitro reconstituted muscle F-actin were made over a wide range of concentrations, 0.01-2 mg/ml F-actin. Measurements of correlation function [g1(t)]2 showed that a transition from a dilute to a semidilute regime for the Brownian motions of filaments occurred at around 0.3 mg/ml F-actin. Beyond this concentration, profiles of successively measured [g1(t)]2 showed very poor reproducibility. This resulted from the existence of very slow components, which could not be measured with a high statistical accuracy even for a measuring time of 3600 s/run. On the other hand, subtraction of these components automatically by an electronic circuit, [g-1(t)]2, or by computer processing, [g1(t)]2, resulted in a fairly good reproducibility of the profiles. The decay characteristics of [g1(t)]2 (and [g-1(t)]2) were very similar to those of [g1(t)]2 for dilute solutions. A theoretical model will be discussed which could account for the above situation. The time sequence [n(t,T)] of photoelectron counts at a sampling time T of light scattered from semidilute solutions of F-actin was stored on magnetic tapes, and both power spectra S(f) and correlation functions [g-1(t)]2 were computed by taking the ensemble average over many short records with duration 1024T. Since both S(f) and [g-1(t)]2 lacked frequency components lower than 1/(2048T) Hz, their profiles were highly reproducible. An analysis of S(f) confirmed our earlier results which had shown an apparent contradiction to later results by a correlation method. A comparison of S(f) and [g-1(t)]2 based on the same [n(t,T)] clarified the reasons why the bandwidth gamma of S(f) largely differed from the bandwidth gamma of [g1(t)]2 and [g-1(t)]2. The temperature dependence of gamma suggested that F-actin would be flexible and that the flexibility parameter would change with temperature.

Actins↗
PubMed2002

Learning generative models of natural images.

This work proposes an unsupervised learning process for analysis of natural images. The derivation is based on a generative model, a stochastic coin-flip process directly operating on many disjoint multivariate Gaussian distributions. Following the maximal likelihood principle and using the Potts encoding, the goodness-of-fit of the generative model to tremendous patches randomly sampled from natural images is quantitatively expressed by an objective function subject to a set of constraints. By further combination of the objective function and the minimal wiring criterion, we achieve a mixed integer and linear programming. A hybrid of the mean field annealing and the gradient descent method is applied to the mathematical framework and produces three sets of interactive dynamics for the learning process. Numerical simulations show that the learning process is effective for extraction of orientation, localization and bandpass features and the generative model can make an ensemble of a sparse code for natural images.

Learning↗
PubMedDate not supplied

Receptive field and orientation scatter studied by tetrode recordings in cat area 17.

The receptive-field positions and orientation preferences of neurons occupying the same tangential location in visual cortex are thought to be similar but to have an associated random scatter. However, previous estimates of this scatter may have been inflated by the use of subjective plotting methods, sequential recording of single units, and residual eye movements. Here we report measurements of receptive-field position and orientation scatter in cat area 17 made with tetrodes, which were able to simultaneously isolate and record up to 11 nearby neurons (ensembles). We studied 355 units at 72 sites with moving light and dark bars. Receptive-field sizes and positions were estimated by least-squares fitting of Gaussians to response profiles. We found that receptive-field position scatter was about half of the ensemble average receptive-field size. We confirmed previous estimates of orientation scatter, but calculations suggested that much of it may be accounted for by anatomical scatter in the positions of recorded neurons relative to the tetrode in a smooth map. Orientation tuning width was positively correlated with the degree of orientation scatter. Scatter was not independent in the two eyes: deviations from the local mean for both preferred orientation and receptive-field position were correlated although a significant amount of residual inter-ocular orientation and receptive-field position scatter was present. We conclude that cortical maps of orientation and receptive-field position are more ordered than was previously thought, and that random scatter in receptive-field positions makes a relatively small contribution to cortical point image size.

Animals↗
PubMed2000

Difference in the mechanisms of the cold and heat induced unfolding of thioredoxin h from Chlamydomonas reinhardtii: spectroscopic and calorimetric studies.

The thermodynamic stability and temperature induced structural changes of oxidized thioredoxin h from Chlamydomonas reinhardtii have been studied using differential scanning calorimetry (DSC), near- and far-UV circular dichroism (CD), and fluorescence spectroscopies. At neutral pH, the heat induced unfolding of thioredoxin h is irreversible. The irreversibly unfolded protein is unable to refold due to the formation of soluble high-order oligomers. In contrast, at acidic pH the heat induced unfolding of thioredoxin h is fully reversible and thus allows the thermodynamic stability of this protein to be characterized. Analysis of the heat induced unfolding at acidic pH using calorimetric and spectroscopic methods shows that the heat induced denaturation of thioredoxin h can be well approximated by a two-state transition. The unfolding of thioredoxin h is accompanied by a large heat capacity change [6.0 +/- 1.0 kJ/(mol.K)], suggesting that at low pH a cold denaturation should be observed at the above-freezing temperatures for this protein. All used methods (DSC, near-UV CD, far-UV CD, Trp fluorescence) do indeed show that thioredoxin h undergoes cold denaturation at pH <2.5. The cold denaturation of thioredoxin h cannot, however, be fitted to a two-state model of unfolding. Furthermore, according to the far-UV CD, thioredoxin h is fully unfolded at pH 2.0 and 0 degrees C, whereas the other three methods (near-UV CD, fluorescence, and DSC) indicate that under these conditions 20-30% of the protein molecules are still in the native state. Several alternative mechanisms explaining these results such as structural differences in the heat and cold denatured state ensembles and the two-domain structure of thioredoxin h are discussed.

Animals↗