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PubMed2003

Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects.

We have applied molecular dynamics umbrella-sampling simulation and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) to calculate the reaction rate of xylose-to- xylulose isomerization catalyzed by xylose isomerase in the presence of two Mg2+ ions. The calculations include determination of the free energy of activation profile and ensemble averaging in the transmission coefficient. The potential energy function is approximated by a combined QM/MM/SVB method involving PM3 for the quantum mechanical (QM) subsystem, CHARMM22 and TIP3P for the molecular mechanical (MM) environment, and a simple valence bond (SVB) local function of two bond distances for the hydride transfer reaction. The simulation confirms the essential features of a mechanism postulated on the basis of kinetics and X-ray data by Whitlow et al. (Whitlow, M.; Howard, A. J.; Finzel, B. C.; Poulos, T. L.; Winborne, E.; Gilliland, G. L. Proteins 1991, 9, 153) and Ringe, Petsko, and coworkers (Labie, A.; Allen, K.-N.; Petsko, G. A.; Ringe, D. Biochemistry 1994, 33, 5469). This mechanism involves a rate-determining 1,2-hydride shift with prior and post proton transfers. Inclusion of quantum mechanical vibrational energy is important for computing the free energy of activation, and quantum mechanical tunneling effects are essential for computing kinetic isotope effects (KIEs). It is found that 85% of the reaction proceeds by tunneling and 15% by overbarrier events. The computed KIE for the ratio of hydride to deuteride transfer is in good agreement with the experimental results. The molecular dynamics simulations reveal that proton and hydride transfer reactions are assisted by breathing motions of the mobile Mg2+ ion in the active site, providing evidence for concerted motion of Mg2+ during the hydride transfer step.

Aldose-Ketose Isomerases↗
PubMed1993

Conformational analysis of protein structures derived from NMR data.

A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of phi, psi, and chi angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline phi angles, alpha-helix phi,psi angles, omega angles, and C alpha chirality. The more lightly restrained torsion angles do show increased clustering as the number of overall experimental observations increases. phi, psi, and chi 1 angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 A. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J-coupling information, stereospecific assignments, and heteronuclear techniques. A suite of programs is being developed to address the special needs of NMR-derived structures which will take into account the existence of increased mobility in solution.

Analysis of Variance↗
PubMed2004

Reward, memory and substance abuse: functional neuronal circuits in the nucleus accumbens.

The firing patterns of neurons in the nucleus accumbens (NA) are examined and discussed with respect to different types of rewards and reward conditions. Comparisons and contrasts between individually identified NA neuron responses to cocaine self-administration and water reinforcement are presented with an emphasis on the fact that the same neurons do not respond in a phasic manner to both types of rewards. However, the phasic firing patterns, even though segregated for each reinforcer, are quite similar, suggesting that the method of differentiation between rewarding stimuli in the NA is by sorting cell populations into distinct ensembles or networks for each type of reinforcer. These neural networks appear to be 'tuned' to respond to particular associative behavioral contexts that couple response execution to reward delivery, and in the process acquire a reciprocity to firing within reward contexts. This maintains the specificity of each reinforcer for the response and associated stimuli that produce it and, makes it possible to attach different NA networks to different reinforcing circumstances. Comparisons of cocaine and water reinforced NA cell firing patterns during rapid switching between these two reinforcers suggests that the networks are negatively coupled and mutually inhibit each other to maintain accurate encoding of immediately experienced, as well as expected (i.e. future) reward contingencies.

Action Potentials↗
PubMed1999

The role of performance tests, manikins and test houses in defining clothing characteristics relevant to risk assessment.

Clothing is an important determinant of human heat exchange and accordingly a critical factor for heat stress risk assessment. A large number of international standards exist concerning protective properties of clothing. However, few standards deal with ergonomic properties and requirements of clothing, making it difficult to evaluate the function of a clothing ensemble in terms of both protection and physiological strain or discomfort. The paper examines existing test methods and procedures for improvement of the situation. Much of the work are presently at research stages, but should in the near future be available for test houses and consumers.

Body Temperature Regulation↗
PubMed2006

Digital concentration readout of single enzyme molecules using femtoliter arrays and Poisson statistics.

Methods for accurately quantifying the concentration of a particular analyte in solution are all based on ensemble responses in which many analyte molecules give rise to the measured signal. In this paper, single molecules of beta-galactosidase were monitored using a 1 mm diameter fiber optic bundle with 2.4 x 10(5) individually sealed, femtoliter microwell reactors. By observation of the buildup of fluorescent products from single enzyme molecule catalysis over the array of reaction vessels and by application of a Poisson statistical analysis, a digital concentration readout was obtained. This approach should prove useful for single molecule enzymology and ultrasensitive bioassays. More generally, the ability to determine concentration by counting individual molecules offers a new approach to analysis of dilute solutions.

Biological Assay↗
PubMed2001

Language and brain: what is up? What is coming up?

The classical aphasiological model of brain/language relationships is nowadays complemented by independent results from functional neuroimaging studies using techniques such as Positron Emission Tomography, functional Magnetic Resonance Imaging, or Event-Related Electro-Encephalography and Magneto-Encephalography mapping. Although brain mapping of language is still hampered by many methodological pitfalls, these methods now appear reliable and provide a renewed description of the temporal spatial dynamics of neural ensembles subserving language functions. Moreover, neuroimaging techniques should also shed a new light on remaining difficult issues such as neural and functional plasticity in developmental or post-lesional contexts.

Aphasia↗
PubMed2002

Stochastic pairwise alignments.

MOTIVATION: The level of sequence conservation between related nucleic acids or proteins often varies considerably along the sequence. Both regions with high variability (mutational hot-spots) and regions of almost perfect sequence identity may occur in the same pair of molecules. The reliability of an alignment therefore strongly depends on the level of local sequence similarity. Especially in regions of high variability, many alignments of almost equal quality exist, and the optimal alignment is highly arbitrary. RESULTS: We discuss two approaches which deal with the inherent ambiguity of the alignment problem based on the computation of the partition function over all canonical pairwise alignments. The ensemble of possible alignments can be described by the probabilities P(ij) of a match between position i in the first and position j in the second sequence. Alternatively, we introduce a probabilistic backtracking procedure that generates ensembles of suboptimal alignments with correct statistical weights. A comparison between structure based alignments and large samples of stochastic alignments shows that the ensemble contains correct alignments with significant probabilities even though the optimal alignment deviates significantly from the structural alignment. Ensembles of suboptimal alignments obtained by stochastic backtracking can be used as input to any bioinformatics method based on pairwise alignment in order to gain reliability information not available from a single optimal alignment. AVAILABILITY: The software described in this contribution is available for downloading at http://www.tbi.univie.ac.at/~ulim/probA/

Algorithms↗
PubMed2001

Molecular dynamics simulations of hard sphere solidification at constant pressure.

Molecular dynamics simulations in the NPT ensemble are used to study the dynamics of crystallization processes in hard sphere systems. The simulation method used permits us to follow the dynamics after a sudden pressure or temperature quench in a one-step process without the need of extra densification methods. During the quench a strong correlation between the system density and the crystalline order parameter Q(6) is found. The growth of fcc order in the system over time is observed in detail and compared to Q(6)(t). We compare results for the equation of state on the metastable fluid branch with previous results from constant volume molecular dynamics simulations. Some results for the crystallization of binary hard sphere mixtures are also presented for a number of different size ratios.

Journal Article↗
PubMed2003

Particle aggregation with simultaneous surface growth.

Particle aggregation with simultaneous surface growth was modeled using a dynamic Monte Carlo method. The Monte Carlo algorithm begins in the particle inception zone and constructs aggregates via ensemble-averaged collisions between spheres and deposition of gaseous species on the sphere surfaces. Simulations were conducted using four scenarios. The first, referred to as scenario 0, is used as a benchmark and simulates aggregation in the absence of surface growth. Scenario 1 forces all balls to grow at a uniform rate while scenario 2 only permits them to grow once they have collided and stuck to each other. The last one is a test scenario constructed to confirm conclusions drawn from scenarios 0-2. The transition between the coalescent and the fully developed fractal aggregation regimes is investigated using shape descriptors to quantify particle geometry. They are used to define the transition between the coalescent and fractal growth regimes. The simulations demonstrate that the morphology of aggregating particles is intimately related to both the surface deposition and particle nucleation rates.

Journal Article↗
PubMed2006

Fusion of Hidden Markov Random Field models and its Bayesian estimation.

In this paper, we present a Hidden Markov Random Field (HMRF) data-fusion model. The proposed model is applied to the segmentation of natural images based on the fusion of colors and textons into Julesz ensembles. The corresponding Exploration/ Selection/Estimation (ESE) procedure for the estimation of the parameters is presented. This method achieves the estimation of the parameters of the Gaussian kernels, the mixture proportions, the region labels, the number of regions, and the Markov hyper-parameter. Meanwhile, we present a new proof of the asymptotic convergence of the ESE procedure, based on original finite time bounds for the rate of convergence.

Algorithms↗
PubMed1999

Single-molecule biomechanics with optical methods.

Single-molecule observation and manipulation have come of age. With the advent of optical tweezers and other methods for probing and imaging single molecules, investigators have circumvented the model-dependent extrapolation from ensemble assays that has been the hallmark of classical biochemistry and biophysics. In recent years, there have been important advances in the understanding of how motor proteins work. The range of these technologies has also started to expand into areas such as DNA transcription and protein folding. Here, recent experiments with rotary motors, linear motors, RNA polymerase, and titin are described.

Biomechanical Phenomena↗
PubMed2004

Nociceptive responses of anterior cingulate cortical ensembles in behaving rats.

OBJECTIVE: To confirm the role of anterior cingulated cortices (ACC) in the coding of pain affect by exploring the neural ensemble coding pattern within the anterior cingulate cortex in behaving rats with a multichannel recording technique. METHODS: In five adult male Sprague-Dawley rats, two arrays of eight stainless steel microwires were bilaterally implanted into ACC. Noxious radiant heat stimulation was applied to the tail, bilateral fore-paws and hind-paws of freely moving rats. Neuroelectric signals were obtained from the microwires and sent to a multichannel recording device via cables and connectors. The time stamps of neuronal activities were stored on a personal computer for off-line analysis. RESULTS: Noxious heat stimuli evoked predominantly excitatory and sustained neural activity within ACC, reflecting the processing of pain unpleasantness; pain-related anticipatory responses could be seen near the stimulation start, indicating the behavioral preparation for escape; ACC neurons had broad receptive fields by showing quite similar pain-related responses to stimuli on either side of the hind-paw, suggesting that they are not eligible for the localization of a stimulus. CONCLUSION: ACC has played a major role in processing the affective-motivational aspect of pain.

Animals↗
PubMed2004

ATP-dependent translocation of proteins along single-stranded DNA: models and methods of analysis of pre-steady state kinetics.

Processive DNA helicases are able to translocate along single-stranded DNA (ssDNA) with biased directionality in a nucleoside triphosphate-dependent reaction, although translocation is not generally sufficient for helicase activity. An understanding of the mechanism of protein translocation along ssDNA requires pre-steady state transient kinetic experiments. Although ensemble experimental approaches have been developed recently for the study of translocation of proteins along DNA, quantitative analysis of the complete time-courses from these experiments, which is needed to obtain quantitative estimates of translocation kinetic parameters (rate constants, processivity, step sizes and ATP coupling) has been lacking. We discuss three ensemble transient kinetic experiments that can be used to study protein translocation along ssDNA, along with the advantages and limitations of each approach. We further describe methods to analyze the complete kinetic time-courses obtained from such experiments performed with a series of ssDNA lengths under "single-round" conditions (i.e. in the absence of re-binding of dissociated protein to DNA). These analysis methods utilize a sequential "n-step" model for protein translocation along ssDNA and enable quantitative determinations of the rate constant, processivity and step size for translocation through global non-linear least-squares fitting of the full time-courses.

Adenosine Triphosphate↗
PubMed2006

Ligation-state hydrogen exchange: coupled binding and folding equilibria in ribonuclease P protein.

Bacillus subtilis ribonuclease P protein (P protein) is predominantly unfolded (D) at physiological pH and low ionic strength; however, small molecule anionic ligands (e.g., sulfate) directly bind to and stabilize the folded state (NL2). Because the D + 2L <--> NL2 transition is experimentally two-state, high-energy states such as the singly bound, folded species (NL) and the unliganded folded species (N) are generally difficult to detect at equilibrium. To study the conformational properties of these ensembles, NMR-detected amide hydrogen exchange (HX) rates of P protein were measured at four sulfate (i.e., ligand) concentrations, a method we denote "ligation-state hydrogen exchange". The ligand concentration dependence of the HX rate of 47 residues was fit to a model with four possible HX pathways, corresponding to the local and/or global opening reactions from NL2 and NL, the local opening of N, and the global opening of N to D. Data analysis permits the calculation of the residue-specific free energy of opening from each ensemble as well as the fractional amide HX flux through each pathway. Results indicate that the predominant route of HX is through the NL and N states, which represent only 0.45% and 0.0005% of the total protein population in 20 mM sodium sulfate, respectively. Despite the low population of N, a region of protected amides was identified. Therefore, exchange through unliganded forms must be accounted for prior to the interpretation of HX-based protein-interaction studies. We offer a simple test to determine if HX occurs through the liganded or unliganded form.

Algorithms↗
PubMed2003

Photolithographically defined deposition of attachment factors as a versatile method for patterning the growth of different cell types in culture.

Spatially defined growth of cells in culture is a useful model for studies ranging from the characterization of cellular motility to the analysis of network behaviour in structurally defined ensembles of excitable cells. Current methodological approaches for obtaining patterned growth include sophisticated modifications of surface chemistry, stamping techniques and microfluidics. The implementation of most of these techniques requires the availability of highly specialized apparatus and some of the methods are specific for certain cell types and/or substrate materials. The goal of the present study was to develop a cell-patterning technique that can be implemented by any laboratory working with cell culture and that is highly adaptable in terms of cell types and substrate materials. The method is based on a photolithographic process that permits the patterned deposition of attachment factors of choice on surfaces previously coated with agar with a spatial resolution (maximal deviation from a straight line) of +/-3 micro m. Because agar efficiently prevents cell adhesion, patterned growth obtained with this technique displays virtually no off-pattern cell attachment. The method permitted the patterning of cardiomyocytes, fibroblasts and HeLa cells on either glass substrates or polymer-coated materials with a spatial resolution of a few micrometers.

Agar↗
PubMed2002

Geometric and chemical patterns of interaction in protein--ligand complexes and their application in docking.

We present a new method for representing the binding site of a protein receptor that allows the use of the DOCK approach to screen large ensembles of receptor conformations for ligand binding. The site points are constructed from templates of what we called "attached points" (ATPTS). Each template (one for each type of amino acid) is composed of a set of representative points that are attached to side-chain and backbone atoms through internal coordinates, carry chemical information about their parent atoms and are intended to cover positions that might be occupied by ligand atoms when complexed to the protein. This method is completely automatic and proved to be extremely fast. With the aim of obtaining an experimental basis for this approach, the Protein Data Bank was searched for proteins in complex with small molecules, to study the geometry of the interactions between the different types of protein residues and the different types of ligand atoms. As a result, well-defined patterns of interaction were obtained for most amino acids. These patterns were then used for constructing a set of templates of attached points, which constitute the core of the ATPTS approach. The quality of the ATPTS representation was demonstrated by using this method, in combination with the DOCK matching and orientation algorithms, to generate correct ligand orientations for >1000 protein--ligand complexes.

Amino Acids↗
PubMed2002

Receptive field structure of neurons in monkey primary visual cortex revealed by stimulation with natural image sequences.

Probing the visual system with the ensemble of signals that occur in the natural environment may reveal aspects of processing that are not evident in the neural responses to artificial stimulus sets, such as conventional bars and sinusoidal gratings. However, unsolved is the question of how to use complex natural stimulation, many aspects of which the experimenter cannot completely specify, to study neural processing. Here a method is presented to investigate the structure of a neuron's receptive field based on its response to movie clips and other stimulus ensembles. As a particular case, the technique provides an estimate of the conventional first-order receptive field of a neuron, similar to what can be obtained with other reverse-correlation schemes. This is demonstrated experimentally and with computer simulations. Our analysis also revealed that the receptive fields of both simple and complex cells had regions where image boundaries, independent of their contrast sign, would enhance or suppress the cell's response. In some cases, these signals were tuned for the orientation of the boundary. This demonstrates for the first time that it might be feasible to investigate the receptive field structure of visual neurons from their responses to natural image sequences.

Animals↗