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PubMed2004

Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method.

The conformational flexibility of a series of diastereomeric cyclic urea HIV-1 protease inhibitors has been examined using the Low Mode:Monte Carlo conformational search method. Force fields were validated by a comparison of the energetic ordering of the minimum energy structures on the AMBER/GBSA(water), OPLSAA/GBSA(water) and HF/6-311G/SCRF(water) surfaces. The energetic ordering of the minima on the OPLSAA /GBSA(water) surface was in better agreement with the quantum calculations than the ordering on the AMBER/GBSA(water) surface. An ensemble of low energy structures was generated using OPLSAA/GBSA(water) and used to compare the molecular shape and flexibility of each diastereomer to the experimentally determined binding affinities and crystal structures of closely related systems. The results indicate that diastereomeric solution-phase energetic stability, conformational rigidity and ability to adopt a chair conformation correlate strongly with experimental binding affinities. Rigid body docking suggests that all of the diastereomers adopt solution-phase conformations suitable for alignment with the HIV-1 protease; however, these results indicate that the binding affinities are dependent upon subtle differences in the P1/P1' and P2/P2' substituent orientations.

Binding Sites↗

PubMed1997

Ionic mechanism of the effects of hydrogen peroxide in rat ventricular myocytes.

1. Whole-cell and amphotericin-perforated patch-clamp techniques have been used to study the effects of hydrogen peroxide (H2O2) on action potentials and underlying ionic currents in single myocytes from the ventricles of adult rat hearts. 2. The results obtained differed markedly depending on the recording method utilized. Conventional whole-cell recordings, in which the myoplasm is dialysed with the contents of the pipette, failed to show any significant effects of H2O2 on the action potential or cell shortening. In contrast, when action potentials were recorded with the amphotericin-perforated patch method, H2O2 (50-200 microM) produced a marked prolongation of the action potential and an increase in cell shortening. 3. Voltage-clamp recordings with the amphotericin-perforated patch method showed that H2O2 caused no significant changes in either the Ca(2+)-independent transient outward K+ current (Ito) or the inwardly rectifying K+ current (IK1). 4. Application of tetrodotoxin (TTX; 8 x 10(-6) M), a Na+ channel blocker, largely inhibited the effects of H2O2 on the action potential. Moreover, anthopleurin A (4 x 10 (-7) M), which augments Na+ current (INa) by slowing its inactivation, mimicked the effects of H2O2 on the action potential of ventricular myocytes. These effects on INa were also blocked almost completely by TTX. 5. The hypothesis that H2O2 can augment INa by slowing its kinetics of inactivation was tested directly using ensemble recordings from cell-attached macropatches. These results demonstrated a significant enhancement of late opening events when H2O2 (200 microM) was included in the recording pipette. A corresponding slowing of inactivation of the ensemble INa was observed. 6. The possibility that protein kinase C (PKC) is an intracellular second messenger for the observed effects of H2O2 was examined using the blocker bisindolylmaelimide (BIS; 10(-7) M). Bath application of BIS prior to H2O2 exposure significantly delayed and also attenuated the development of the action potential prolongation. 7. These results demonstrate marked electrophysiological effects of H2O2 in rat ventricle. The dependence of these effects on recording methods suggests involvement of an intracellular second messenger, and the results with the PKC inhibitor, BIS, support this possibility. The most prominent effect of H2O2 on the ionic currents which underlie the action potential is a slowing of inactivation of the TTX-sensitive INa. Recent molecular studies have demonstrated a PKC phosphorylation site on the rat cardiac Na+ channel isoform and have also shown that PKC activation can slow inactivation of INa.

Action Potentials↗

PubMed1979

Interactions among an ensemble of chordotonal organ receptors and motor neurons of the crayfish claw.

1. Action potentials of crayfish propodite-dactyl (PD) chordotonal organ receptors and two claw motor neurons, the opener inhibitor (OI) and slow closer excitor CE) were simultaneously monitored during imposed step and ramp movements of the dactyl or while the dactyl was held at various positions. 2. The activities of the cells during imposed displacements were analyzed using peristimulus time histograms and response and contour planes. The proprioceptive fields (PFs) of individual receptors resemble components of the more complex motor neuron PFs. Some receptors are briefly active after each successive opening step, while others do not respond to steps near the closed position but respond as the joint angle increases, becoming active when the claw is held open. Another type of receptor responds to closing movements. 3. Interactions among the various types of receptors and the two motor neurons were detected and analyzed by various statistical methods and intracellular recording techniques. The results indicate that receptors activated during opening movements and when the dactyl is held at open positions excite OI and CE via divergent functional connections. The efficacies of the connections made by a receptor may differ. Receptors activated by closing movements produce hyperpolarizing synaptic potentials in both efferents, possible directly or via interneurons. 4. It is concluded that several types of chordotonal organ receptors form an ensemble of parallel input channels, which modulates the activities of OI and CE and contributes to the generation of the spatial-temporal nonuniformities of their proprioceptive reflex responses.

Animals↗

PubMed2007

Towards in silico lead optimization: scores from ensembles of protein/ligand conformations reliably correlate with biological activity.

Accurately ranking protein/ligand interactions and distinguishing subtle differences between homologous compounds in a virtual focused library in silico is essential in a structure-based drug discovery program. In order to establish a predictive model to design novel inhibitors of dihydrofolate reductase (DHFR) from the parasitic protozoa, Cryptosporidium hominis, we docked a series of 30 DHFR inhibitors with measured inhibition constants against the crystal structure of the protein. By including protein flexibility and averaging the energies of the 25 lowest protein/ligand conformers we obtained more accurate total nonbonded energies from which we calculated a predicted biological activity. The calculated and measured biological activities showed reliable correlations of 72.9%. Additionally, visual analysis of the ensemble of protein/ligand conformations revealed alternative ligand binding pockets in the active site. Using the same principles we then created a homology model of DHFR from Toxoplasma gondii and docked 11 inhibitors. A correlation of 50.2% between docking score and activity validates both the method and the model. The correlations presented here are particularly compelling considering the high structural similarity of the ligands and the fact that we have used structures derived from crystallographic data and homology modeling. These docking principles may be useful in any lead optimization study where accurate ranking of similar compounds is desired.

Algorithms↗

PubMed1982

Statistical and dimensional analysis of the neural representation of the acoustic biotope of the frog.

The field of investigation is the neural representation of acoustic stimuli occurring in the natural environment of the frog. The point of departure is the description of a stimulus ensemble consisting of natural sounds: the acoustic biotope. A relation of statistical and dimensional structure of the acoustic biotope is indicated. The animal used in the neurophysiological experiments is the grass frog, Rana temporaria L.; microelectrode recordings are made in the auditory midbrain. A method is described to determine the existence of a relation between acoustic stimulus and neural events. The form of this relation has been investigated by first- and second-order stimulus-event correlation. While the first one does not give significant results, the second one leads to the spectrotemporal receptive field of the neuron for natural stimuli. Questions are formulated to estimate the value of this receptive field as a functional descriptor of the neuron. Finally, an outline is sketched for a synthetic construction of the bioacoustic space from neuroacoustic subspaces.

Acoustic Stimulation↗

PubMed2000

Objective comparison of protein structures: error-scaled difference distance matrices.

Understanding of macromolecular function in many cases relies on the comparison of related structural models. Commonly used least-squares superposition methods suffer from bias introduced into the comparison process by the subjective choice of atoms employed for the superposition. Difference distance matrices are a more objective means of comparing structures as they do not depend on a particular superposition scheme. However, they suffer from very high noise originating from coordinate errors. Modern refinement programs allow the rigorous estimation of standard uncertainties for individual atomic positions. These errors can be propagated through the calculation of a difference distance matrix allowing one to assess the significance level of structural differences. An algorithm is presented which produces an intuitive graphical representation of difference distance matrices after normalization to their error levels. Two examples where its application was revealing are described. Alternatives are suggested for cases where rigorous estimation of individual errors by the inversion of the full least-squares matrix is not feasible. The method offers an unbiased way to detect significant similarities and differences between related structures, as encountered in studies of complexes and mutants or when multiple models are obtained from experiments such as crystal structures involving non-crystallographic symmetry or different crystal modifications, or ensembles derived from NMR spectroscopy.

Anti-Bacterial Agents↗

PubMed2025

Replication and Functional Prediction of Two GWAS-Reported SNPs Located on RAD50 Gene Associated with Asthma in Pakistani Children.

BACKGROUND: Genome-wide association studies (GWAS) have indicated that several single nucleotide variants (SNVs) of the RAD50 gene are significantly associated with childhood-onset asthma. However, the biological role of RAD50, and its genomic variants that predispose individuals to asthma, remains unclear. This case-control study aimed to investigate the association of two Single nucleotide polymorphisms (SNPs) rs2244012, and rs6871536 of RAD50 with asthma susceptibility using experimental and computational tools. METHODS: The case-control study involved 355 participants: "176 asthma cases [mean age (sd) = 8.91 ±3.05] and 179 healthy controls [mean age (sd) = 11.10 ±8.86] from local Punjabi population of Pakistan. The SNPs were analyzed using a modified single base extension method. The allelic association with asthma and linkage disequilibrium (LD) between the two main SNPs were performed using the SHEsis tool. SNPStats was used to assess the association of SNPs under genotypic models and interaction with non-genetic factors. The LD calculator of ENSEMBL employed for the identification of proxy SNPs in high LD (r^2 > 0.97) to main SNPs. Additionally, HaploReg(v4.1) was utilized to gauge the impact of SNPs on genomic regulations. RESULTS: In current study, both SNPs were found to have a significant association (p-value <0.05) with childhood-onset asthma development under allelic and genotypic models. The alternative "G" allele of rs2244012 is shown to modify two regulatory motifs: Nrf-2 and Zbtb12, while the alternative "C" allele of rs6871536 is predicted to alter the OSF-2 motif. Moreover, 10 SNVs proximal to rs2244012 and 21 SNVs near rs6871536 are in high LD in the Punjabi population of Lahore, Pakistan (PJL). These proxy/high-LD SNVs also displayed the potential to change DNA regulatory motifs. CONCLUSION: the rs2244012, and rs6871536 variants of RAD50 gene are significantly association with childhood asthma in Pakistan. Despite being intronic variants, it is our inference that these two SNPs have the potential to either independently or synergistically regulate inflammatory responses via nearby SNVs.

Asthma↗

PubMed2005

Interactive measurement and characterization of DNA molecules by analysis of AFM images.

BACKGROUND: In the past few years, computer-based analysis of atomic-force microscopic images has acquired increasing importance for studying biomolecules such as DNA. On the one hand, fully automated methods do not allow analysis of complex shapes; on the other hand, manual methods are usually time consuming and inaccurate. The semiautomated approach presented in this report overcomes the drawbacks of both methods. METHODS: Two kinds of images were analyzed: computer-generated filaments that modeled circular DNA molecules on a surface and real atomic-force microscopic images of DNA molecules adsorbed on an appropriate substrate surface. RESULTS: The algorithm was tested on a group of 140 simulated and 189 real plasmids with a nominal length of 913 nm. The accuracy of the length measurement was statistically evaluated on the ensemble of molecules, with particular attention to the influence of the noise. Mean contour lengths of 912 +/- 5 nm and 910 +/- 47 nm were found for simulated and real plasmids, respectively. The measured end-to-end distance of lambda-DNA molecules as a function of their contour length is reported, from which it is possible to estimate the stiffness of the DNA molecules adsorbed onto a surface; the value obtained for the DNA persistence length (42 +/- 5 nm) is consistent with values measured by other imaging techniques. CONCLUSIONS: An interactive algorithm for DNA molecule measurements based on the detection of the filament ridge line in a digitized image is presented. The simulation of artificial filaments combined with the experimental data demonstrates that the proposed method can be a valuable tool for the DNA contour length evaluation, especially in the case of complex shapes where the use of automatic methods is not possible.

Algorithms↗

PubMed2002

Nonlinear phase desynchronization in human electroencephalographic data.

Ensembles of coupled nonlinear systems represent natural candidates for the modeling of brain dynamics. The objective of this study is to examine the complex signal produced by coupled chaotic attractors, to discuss their potential relevance to distributed processes in the brain, and to illustrate a method of detecting their contribution to human EEG morphology. Two measures of quantifying the behavior of coupled nonlinear systems are presented: a measure of phase synchrony and a novel measure of intermittent phase desynchronization. These are used to quantify the behavior of numerical examples of coupled chaotic attractors. Experimental evidence of their contribution to the morphology of the human alpha rhythm is then illustrated in a study of EEG recordings from 40 healthy human subjects. Amplitude-adjusted phase-randomized surrogate data is used to test the null hypothesis that the observed patterns of phase coherence can be described by purely linear methods. Statistical analysis reveals that this null hypothesis can be robustly rejected in a small number (approximately 4%) of EEG epochs. These findings are discussed with reference to the adaptive function and complex dynamics of the brain.

Adult↗

PubMed1999

A tracing evoked potential estimator.

The paper presents an adaptive Gaussian radial basis function neural network (RBFNN) for rapid estimation of evoked potential (EP). Usually, a recorded EP is severely contaminated by background ongoing activities of the brain. Many approaches have been reported to enhance the signal-to-noise ratio (SNR) of the recorded signal. However, non-linear methods are seldom explored due to their complexity and the fact that the non-linear characteristics of the signal are generally hard to determine. An RBFNN possesses built-in non-linear activation functions that enable the neural network to learn any function mapping. An RBFNN was carefully designed to model the EP signal. It has the advantage of being linear-in-parameter, thus a conventional adaptive method can efficiently estimate its parameters. The proposed algorithm is simple so that its convergence behaviour and performance in signal-to-noise ratio (SNR) improvement can be mathematically derived. A series of experiments carried out on simulated and human test responses confirmed the superior performance of the method. In a simulation experiment, an RBFNN having 15 hidden nodes was trained to approximate human visual EP (VEP). For detecting human brain stem auditory EP (BAEP), the approach (40 hidden nodes and convergence rate = 0.005) speeded up the estimation remarkably by using only 80 ensembles to achieve a result comparable to that obtained by averaging 1000 ensembles.

Electroencephalography↗

PubMed1995

Calculation of oxygen pressures in tissue with anisotropic capillary orientation. II. Coupling of two-dimensional planes.

The mathematical descriptions of oxygen transport in terms of two-dimensional diffusion in planes perpendicular to the capillaries can be coupled for an ensemble of planes to yield a three-dimensional description. In tissue with a distinct orientation of the oxygen supplying structures, the capillaries, this leads to a description of oxygen pressure in a whole tissue volume. Muscle tissue is an example of such tissue. The method allows calculation of oxygen pressure (pO2) at any location in the volume. Tissue volume oxygen status can be assessed by constructing a pO2 histogram, gathering pO2's at a large number of locations in the tissue.

Animals↗

PubMed2004

Modeling the resolution and sensitivity of FAIMS analyses.

Field asymmetric waveform ion mobility spectrometry (FAIMS) is rapidly gaining acceptance as a robust, versatile tool for post-ionization separations prior to mass-spectrometric analyses. The separation is based on differences between ion mobilities at high and low electric fields, and proceeds at atmospheric pressure. Two major advantages of FAIMS over condensed-phase separations are its high speed and an ion focusing effect that often improves sensitivity. While selected aspects of FAIMS performance are understood empirically, no physical model rationalizing the resolving power and sensitivity of the method and revealing their dependence on instrumental variables has existed. Here we present a first-principles computational treatment capable of simulating the FAIMS analyzer for virtually any geometry (including the known cylindrical and planar designs) and arbitrary operational parameters. The approach involves propagating an ensemble of ion trajectories through the device in real time under the influence of applied asymmetric potential, diffusional motion incorporating the high-field and anisotropic phenomena, and mutual Coulomb repulsion of ionic charges. Calculations for both resolution and sensitivity are validated by excellent agreement with measurements in different FAIMS modes for ions representing diverse types and analyte classes.

Amino Acids↗

PubMed2006

On a probabilistic model for the numerical estimation of nocturnal migration of birds.

The study of nocturnal bird migration by cone methods of observation has a century-long history but has continued to be used up to the present. To describe the flux and estimate the number of passing birds a probabilistic model is proposed. This model is based on the concept of dynamic Poisson ensemble of points in appropriate phase space and has two parameters. One is scalar and the other one is functional. We constructed consistent estimations of these parameters and discuss their use for the numerical estimation of the flux of birds observed in a narrow light cone generated by the bright lunar disk and formed by an open angle of telescope. Selection on the same type of birds was suggested as the necessary condition for the model application. Ground speed of each bird was introduced into the model as a new but obligatory value determining the quantification of the flux of bird.

Animal Migration↗

PubMed2002

A computer simulation of functional group contributions to free energy in water and a DPPC lipid bilayer.

A series of all-atom molecular dynamics simulations has been performed to evaluate the contributions of various functional groups to the free energy of solvation in water and a dipalmitoylphospatidylcholine lipid bilayer membrane and to the free energies of solute transfer (Delta(DeltaG(o))X) from water into the ordered-chain interior of the bilayer. Free energies for mutations of the alpha-H atom in p-toluic acid to six different substituents (-CH3, -Cl, -OCH3, -CN, -OH, -COOH) were calculated by a combined thermodynamic integration and perturbation method and compared to literature results from vapor pressure measurements, partition coefficients, and membrane transport experiments. Convergence of the calculated free energies was indicated by substantial declines in standard deviations for the calculated free energies with increased simulation length, by the independence of the ensemble-averaged Boltzmann factors to simulation length, and the weak dependence of hysteresis effects on simulation length over two different simulation lengths and starting from different initial configurations. Calculated values of Delta(DeltaG(o))X correlate linearly with corresponding values obtained from lipid bilayer transport experiments with a slope of 1.1 and from measurements of partition coefficients between water and hexadecane or decadiene, with slopes of 1.1 and 0.9, respectively. Van der Waals interactions between the functional group of interest and the acyl chains in the ordered chain region account for more than 95% of the overall potential energy of interaction. These results support the view that the ordered chain region within the bilayer interior is the barrier domain for transport and that solvation interactions within this region resemble those occurring in a nonpolar hydrocarbon.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1998

Efficient dynamics in the space of contact maps.

BACKGROUND: Two problems are of major importance in protein fold prediction: how to generate plausible conformations, and how to choose an energy function to identify the native state. Contact maps are a simple representation of protein structure and offer a promising framework to address these two issues. RESULTS: In this work we develop Monte Carlo dynamics in contact map space. The procedure is divided into four steps: non-local dynamics, in which large-scale "cluster" moves are performed (clusters are in approximate correspondence with secondary structure elements); local dynamics, in which secondary structure location is optimized; reconstruction, in which the physicality of the contact map is restored; and refinement, which consists of a further Monte Carlo energy minimization in real space. We demonstrate that such a dynamical procedure is effective in producing uncorrelated low-energy states. CONCLUSIONS: The procedure introduced in this paper very effectively generates a representative ensemble of conformations. We are able to show that existing sets of pairwise contact energy parameters are not suitable to single out the native state within this ensemble. The remaining outstanding issue in protein folding is to find an energy function that can discriminate the native state from decoys.

Models, Chemical↗

PubMed2006

Low-temperature vapor-liquid equilibria from parallelized molecular dynamics simulations. Application to 1- and 2-methylnaphthalene.

A parallelized sampling version of the Gibbs Ensemble (Mol. Phys. 2000, 98, 1887) has been implemented to predict low-temperature vapor-liquid equilibria of 1- and 2-methylnaphthalene modeled by anisotropic united atom potentials. The simulation were performed at the low temperature of 364.2 K at which common direct simulation methods fail due to particle transfer problems. The simulation results are compared with published results obtained from the Gibbs-Duhem integration method and with experimental data. Both methods are compared and discussed in terms of computational efficiency and with respect to their future use at other thermodynamic conditions.

Journal Article↗

PubMed2004

Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations.

We present an adaptive algorithm which optimizes the statistical-mechanical ensemble in a generalized broad-histogram Monte Carlo simulation to maximize the system's rate of round trips in total energy. The scaling of the mean round-trip time from the ground state to the maximum entropy state for this local-update method is found to be O ( [N ln N](2) ) for both the ferromagnetic and the fully frustrated two-dimensional Ising model with N spins. Our algorithm thereby substantially outperforms flat-histogram methods such as the Wang-Landau algorithm.

Journal Article↗

PubMed2005

Interplay between chemical reactions and transport in structured spaces.

The main motivation behind this study is to understand the interplay between the reactions and transport in a geometries that are not compact. Typical examples of compact geometries are a box or a sphere. A network made of containers C(1) , C(2),..., C(N) and tubes is an example of the space that is structured and noncompact. In containers, particles react with the rate lambda. Tubes connecting containers allow for the exchange of chemicals with the transport rate D. A situation is considered where a number of reactants is small and kinetics is noise dominated. A method is presented that can be used to calculate the average and higher moments of the reaction time. A number of different chemical reactions are studied and their performance compared in various ways. Two schemes are discussed in general, the reaction on a fixed geometry ensemble (ROGE) and the geometry on a fixed reaction ensemble, examples are given in the ROGE case. The most important findings are as follows. (i) There is a large number of reactions that run faster in a networklike geometry. Such reactions contain antagonistic catalytic influences in the intermediate stages of a reaction scheme that are best dealt with in a networklike structure. (ii) Antagonistic catalytic influences are hard to identify since they are strongly connected to the pattern of injected molecules (inject pattern) and depend on the choice of molecules that have to be synthesized at the end (task pattern). (iii) The reaction time depends strongly on the details of the inject and task patterns.

Algorithms↗