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PubMed2004

Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein.

The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovine acyl-coenzyme A binding protein (ACBP) at three different concentrations of guanidine hydrochloride. As the experimentally determined distance information corresponds to weighted averages over a broad ensemble of structures, we applied the experimental restraints to a system of noninteracting replicas of the protein by using a Monte Carlo sampling scheme. This procedure permits us to sample ensembles of conformations that are compatible with the experimental data and thus to obtain information regarding the distribution of structures in the denatured state. Our results show that the denatured state of ACBP is highly heterogeneous. The high sensitivity of the computational method that we present, however, enabled us to identify long-range interactions between two regions, located near the N- and C-termini, that include both native and non-native elements. The preferential formation of these contacts suggests that the sequence-dependent patterns of helical propensity and hydrophobicity are important determinants of the structure in the denatured state of ACBP.

Acyl Coenzyme A↗
PubMed2005

On the computational calculation of surface free energies for the disordered semihexagonal reconstructed Au(100) surface.

Previously we developed a general method for calculating the free energy of any surface constrained to a distinct surface excess number/density. In this paper we show how to combine a range of such surfaces, whose free energies have been calculated, to produce an ad hoc semigrand canonical ensemble of surfaces from which ensemble surface properties can be calculated, including the ensemble surface free energy. We construct such an ensemble for the disordered Au(100) semihexagonal reconstructed surface using a Glue model potential at 1000 K and calculate the ensemble surface free energy to be 0.088 18 eVA(2). The ensemble average surface lateral density was found to be 1.375 (with respect to the bulk), which is in agreement with previous grand canonical Monte Carlo studies.

Journal Article↗
PubMed2002

Large scale cross-correlations in Internet traffic.

The Internet is a complex network of interconnected routers, and the existence of a collective behavior such as congestion suggests that the correlations between the different connections play a crucial role. It is thus critical to measure and quantify these correlations. We use methods of random matrix theory (RMT) to analyze the cross-correlation matrix C of information flow changes of 650 connections between 26 routers of the French scientific network "Renater." We find that C has the universal properties of the Gaussian orthogonal ensemble of random matrices: The distribution of eigenvalues-up to a rescaling that exhibits a typical correlation time of the order of 10 min-and the spacing distribution follow the predictions of RMT. There are some deviations for large eigenvalues which contain network-specific information and which identify genuine correlations between the connections. The study of the most correlated connections reveals the existence of "active centers" that are exchanging information with a large number of routers thereby inducing correlations between the corresponding connections. These strong correlations could be a reason for the observed self-similarity in the world-wide web traffic.

Journal Article↗
PubMed1994

Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography.

Time-averaged structure-factor restraints have been used in two molecular dynamics refinement schemes to define ensembles of conformations for myoglobin that fit the experimentally measured Bragg scattering from P6 crystals. The geometries of the structures have been maintained to the same currently acceptable limits in all cases. Free R value analysis was used to assess the validity of the two approaches. In the first scheme, where atoms have no B values, the decrease in R value was found to be spurious as judged by a concomitant increase in the free R value. The other scheme, however, which retains individual B values, was found to yield both low R values and low free R values; thus, here the additional variables introduced by modeling the protein in terms of an evolving ensemble of states do not overfit the data. For comparison, refinements were also carried out on the system using several other techniques for isotropic and anisotropic crystallographic refinement. The time-averaged refinements with B values compare quite favorably with the standard methods, but yield additional information about substates of the system. Hence, correctly applied time-averaged refinements can yield accurate models for protein molecules; moreover, by essentially relaxing the harmonic approximation from the refinement process, these refinements allow a more detailed description of the motions of complex molecules, such as proteins, to be determined from X-ray crystallographic data.

Journal Article↗
PubMed1996

Maximum likelihood analysis of cardiac late potentials.

This study presents a new time-domain method for the detection of late potentials in individual leads. Basic statistical properties of the ECG samples are modeled in order to estimate the amplitude and duration of late potentials. The signal model accounts for correlation in both time and across the ensemble of beats. Late potentials are modeled as a colored process with unknown amplitude which is disturbed by white, Gaussian noise. Maximum likelihood estimation is applied to the model for estimating the amplitude of the late potentials. The resulting estimator consists of an eigenvector-based filter followed by a nonlinear operation. The performance of the maximum likelihood procedure was compared to that obtained by traditional time-domain analysis based on the vector magnitude. It was found that the new technique yielded a substantial improvement of the signal-to-noise ratio in the function used for endpoint determination. This improvement leads to a prolongation of the filtered QRS duration in cases with late potentials.

Action Potentials↗
PubMed2005

Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.

An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and their combination with molecular dynamics simulations. For neurotensin, a peptide that binds with high affinity to a G-protein coupled receptor, this method permits the investigation of the changes in conformational preferences of a neurotransmitter transferred from a frozen aqueous solution via a lipid model phase to the receptor-bound form. The results speak against a conformational pre-organization of the ligand in detergents in which the receptor has been shown to be functional. Further extensions to the study of protein folding are possible.

Detergents↗
PubMed2004

Evaluation of multiple models to distinguish closely related forms of disease using DNA microarray data: an application to multiple myeloma.

MOTIVATION: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is anticipated that this information can also be used to develop molecular diagnostic models and to provide insight into mechanisms of disease progression, e.g., transition from healthy to benign hyperplasia or conversion of a benign hyperplasia to overt malignancy. However, standard data analysis techniques are not trivial to employ on these large data sets. Methodology designed to handle large data sets (or modified to do so) is needed to access the vital information contained in the genetic samples, which in turn can be used to develop more robust and accurate methods of clinical diagnostics and prognostics. RESULTS: Here we report on the application of a panel of statistical and data mining methodologies to classify groups of samples based on expression of 12,000 genes derived from a high density oligonucleotide microarray analysis of highly purified plasma cells from newly diagnosed MM, MGUS, and normal healthy donors. The three groups of samples are each tested against each other. The methods are found to be similar in their ability to predict group membership; all do quite well at predicting MM vs. normal and MGUS vs. normal. However, no method appears to be able to distinguish explicitly the genetic mechanisms between MM and MGUS. We believe this might be due to the lack of genetic differences between these two conditions, and may not be due to the failure of the models. We report the prediction errors for each of the models and each of the methods. Additionally, we report ROC curves for the results on group prediction. AVAILABILITY: Logistic regression: standard software, available, for example in SAS. Decision trees and boosted trees: C5.0 from www.rulequest.com. SVM: SVM-light is publicly available from svmlight.joachims.org. Naïve Bayes and ensemble of voters are publicly available from www.biostat.wisc.edu/~mwaddell/eov.html. Nearest Shrunken Centroids is publicly available from http://www-stat.stanford.edu/~tibs/PAM.

Journal Article↗
PubMed2006

Development of a collimator blurring compensation method using fine angular sampling projection data in SPECT.

Due to the collimator aperture, spatial resolution of SPECT data varies with source-to-detector distance. Since the radius of detector rotation is bigger when scanning larger patients, spatial resolution is degraded in these cases. Emitted gamma rays travel not only along the central axis of the collimator hole but also off-axis due to the collimator aperture. However, an off-axis ray at one angle would be a central-axis ray at another angle; therefore, raw projection data at one angle can be thought of as an ensemble of central-axis rays collected from a small arc equal to the collimator aperture. Thus, fine angular sampling can compensate for collimator blurring. By using a sampling pitch of less than half the collimator aperture angle, compensation was performed by subtracting the weighted sum of the projection data from the raw projection data. Collimator geometry and detector rotation radius determined the weighting function. Cylindrical phantom with four different-sized rods and torso phantom for Tl-201 cardiac SPECT simulation were used for evaluation. Aperture angle of the collimator was 7 degrees. Projection sampling pitch was 2 degrees. In both phantom studies, the proposed method showed improvement in contrast and reduction of partial volume effect, thereby indicating that the proposed method can compensate adequately for image blurring caused by the collimator aperture.

Artifacts↗
PubMed1997

Molecular complementarity II: energetic and vectorial basis of biological homeostasis and its implications for death.

The energetic basis of molecular complementarity is presented. In biological systems requiring both homeostasis and non-equilibrium state maintenance, molecular complementarity provides a framework for the co-existence of these states within an organism. Smoothly changing homeostatic and thermodynamic systems, such as regulation of pH or an ensemble of asynchronous muscle crossbridges, are modeled using Liapunov functions. When biological systems undergo discontinuous state changes, such as the initiation of the heartbeat, life/death transition or the detachment of molecules, alternative analytical systems such as catastrophe theory provide information that continuous analytical methods cannot. Catastrophe theory produces a model of biology in which death can occur by two distinct mechanisms: loss of homeostatic control or loss of sufficient free energy. Molecular complementarity buffers molecules from temporal and physical changes. The usefulness of molecular complementarity is limited to association energies near the ambient energy, kT. Within this range, complementarity will alter molecular functions and will convert scalar biochemical reactions into vectorial physiological processes. Both thermodynamic and catastrophic models can be used to link energetic and homeostatic processes: the former providing quantitative information from continuous systems; the latter providing qualitative information from discontinuous systems involving state changes.

Animals↗
PubMed1984

System identification of human stretch reflex dynamics: tibialis anterior.

System identification methods have shown that the stretch reflex in the human ankle extensor (triceps surae, TS) may be modeled as velocity feedback via a single, short latency pathway containing a uni-directional rate-sensitive nonlinearity. Evidence of differences in the reflex organization in flexors and extensors led us to use the same methods to examine stretch reflexes in the ankle flexor (tibialis anterior, TA). Five normal subjects maintained a tonic contraction of TA while subjected to repeated, stochastic perturbations of ankle position. Position, torque, and smoothed, rectified EMGs from TA and TS were recorded and ensemble averaged over 25 stimulus presentations. Linear impulse response functions relating TA EMG to ankle velocity were then determined. The results confirmed the existence of significant differences between stretch reflexes in TA and TS. In particular: 1. TA impulse response functions were characterized by two distinct peaks of excitation separated by a period of inhibition. The impulse response function amplitude increased with increasing mean torque and decreased with displacement amplitude although the sensitivity of the two peaks to these changes was different. This was interpreted as suggesting that TA stretch reflexes involve two separate pathways both involving muscle spindle information. 2. TA stretch reflexes modulate tonic activity much less than do those in TS. 3. The strong uni-directional rate-sensitive nonlinearity seen in TS was not present in TA. The functional significance of these differences remains to be determined.

Adult↗
PubMed2001

Estimating synaptic parameters from mean, variance, and covariance in trains of synaptic responses.

Fluctuation analysis of synaptic transmission using the variance-mean approach has been restricted in the past to steady-state responses. Here we extend this method to short repetitive trains of synaptic responses, during which the response amplitudes are not stationary. We consider intervals between trains, long enough so that the system is in the same average state at the beginning of each train. This allows analysis of ensemble means and variances for each response in a train separately. Thus, modifications in synaptic efficacy during short-term plasticity can be attributed to changes in synaptic parameters. In addition, we provide practical guidelines for the analysis of the covariance between successive responses in trains. Explicit algorithms to estimate synaptic parameters are derived and tested by Monte Carlo simulations on the basis of a binomial model of synaptic transmission, allowing for quantal variability, heterogeneity in the release probability, and postsynaptic receptor saturation and desensitization. We find that the combined analysis of variance and covariance is advantageous in yielding an estimate for the number of release sites, which is independent of heterogeneity in the release probability under certain conditions. Furthermore, it allows one to calculate the apparent quantal size for each response in a sequence of stimuli.

Analysis of Variance↗
PubMed2001

Screening of ion channel receptor agonists using capillary electrophoresis-patch clamp detection with resensitized detector cells.

Efficient techniques for identifying endogenous and synthetic ligands of ion channels are important in understanding neuronal communication and for screening drug libraries. This paper describes a technique based on capillary electrophoresis (CE) separation coupled to patch-clamp (PC) detection where a pulsed-flow superfusion scheme was implemented for improved detection. The nicotinic acetylcholine receptor (nAChr) agonists acetylcholine, carbachol, and (-)-nicotine were fractionated and detected by patch-clamped pheochromcytoma detector cells. The high-conductance state of the nAChr during CE-PC detection was maintained and repetitively resensitized using pulsed-flow superfusion with agonist-free buffer. In this way, each agonist evoked an ensemble of peak currents that reflected the spatiotemporal distribution for the ligand at the cell surface. The technique takes advantage of the intrinsic high selectivity and sensitivity of membrane-expressed receptors and allowed for resolution and identification of closely migrating ligands. The method was employed for determination of acetylcholine content in cell lysates.

Acetylcholine↗
PubMed2003

Relative influence of hydrophobicity and net charge in the aggregation of two homologous proteins.

A potentially amyloidogenic protein has to be at least partially unfolded to form amyloid aggregates. However, aggregation of the partially or totally unfolded state of a protein is modulated by at least three other factors: hydrophobicity, propensity to form secondary structure, and net charge of the polypeptide chain. We propose to evaluate the relative importance of net charge, as opposed to the other factors, on protein aggregation and amyloidogenicity. For this aim, we have used two homologous proteins that were previously shown to be able to form amyloid fibrils in vitro, the N-terminal domain of HypF from Escherichia coli (HypF-N) and human muscle acylphosphatase (AcP). The aggregation process from an ensemble of partially unfolded conformations is ca. 1000-fold faster for HypF-N than for AcP. This difference can mainly be attributed to a higher hydrophobicity and a lower net charge for HypF-N than for AcP. By using protein engineering methods, we have decreased the net charge of AcP to a value identical to that of wild-type HypF-N and increased the net charge of HypF-N to a value identical to that of wild-type AcP. Amino acid substitutions were selected to minimize changes in hydrophobicity and secondary structure propensities. We were able to estimate that the difference in net charge between the two wild-type proteins contributes to 20-25% of the difference in their aggregation rates. An understanding of the relative influences of these forces in protein aggregation has implications for elucidating the complexity of the aggregation process, for predicting the effect of natural mutations, and for accurate protein design.

Acid Anhydride Hydrolases↗
PubMed2004

Highly specific and accurate selection of siRNAs for high-throughput functional assays.

MOTIVATION: Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity. Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date, the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs. RESULT: Here, we present a program that for the first time completely automates the search for siRNAs. In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method. After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, which can cause cross-hybridization, are checked in databases containing a unique entry for each gene. These truly non-redundant databases are constructed from the genome annotations (Ensembl). Also intron/exon boundaries, presence of polymorphisms (single nucleotide polymorphisms) specificity for either gene or transcript, and other features can be selected to be considered in the design of siRNAs. AVAILABILITY: The program is available as a web server at http://side.bioinfo.cnio.es. The program was written under the GPL license. CONTACT: jdopazo@cnio.es.

Algorithms↗
PubMed2004

Specular neutron reflectivity and the structure of artificial protein maquettes vectorially oriented at interfaces.

Artificial peptides can be designed to possess a variety of functionalities. If these peptides can be ordered in an ensemble, the functionality can impart macroscopic material properties to the ensemble. Neutron reflectivity is shown to be an effective probe of the intramolecular structures of such peptides vectorially oriented at an interface, key to ensuring that the designed molecular structures translate into the desired material properties of the interface. A model-independent method is utilized to analyze the neutron reflectivity from an alkylated, di- alpha -helical peptide, containing perdeuterated leucine residues at one or two pre-selected positions, in mixed Langmuir monolayers with a phospholipid. The results presented here are more definitive than prior work employing x-ray reflectivity. They show explicitly that the di-helical peptide retains its designed alpha -helical secondary structure at the interface, when oriented perpendicular to the interface at high surface pressure, with the helices projecting into the aqueous subphase without penetrating the layer of phospholipid headgroups.

Lipid Bilayers↗
PubMed2003

Prevention of the adverse photic effects of peripheral light-focusing using UV-blocking contact lenses.

PURPOSE: Peripheral light-focusing (PLF) is an occult form of ultraviolet radiation (UVR) hazardous to the human eye. In PLF, obliquely incident light is refracted from the peripheral cornea to concentrated sites inside the anterior segment. In the current study, the directionality of this phenomenon for UVR and whether PLF is established in outdoor settings exposed to sunlight were investigated. The protection provided by a UV-blocking contact lens was also evaluated. METHODS: UVA and UVB sensors were placed on the nasal limbus of an anatomically based model eye. The temporal limbus was exposed to a UV light source placed at various angles behind the frontal plane. PLF was quantified with the sensor output. The ensemble was mounted in the orbit of a mannequin head and exposed to sunlight in three insolation environments within the region of Sydney, Australia. PLF for UVA and UVB was determined with no eyewear or with sunglasses and commercially available soft contact lenses, with and without UV-blocking capability. RESULTS: The intensity of UVA peaked at approximately 120 degrees incidence, the level at which the UVB response was also at its maximum. The intensification of UVA was up to x18.3. The intensity of PLF for UVA and UVB was reduced by an order of magnitude by a UV-blocking contact lens, whereas a clear contact lenses had a much lesser effect. Only the UV-blocking contact lens achieved a significant effect on UVA and UVB irradiance in the urban, beach, and mountain locales (P < 0.056). CONCLUSIONS: The results identify another type of sunlight hazard: the peripheral focusing of obliquely incident light. UVR from albedo (reflected ambient light) is capable of establishing PLF in the anterior segment, but this can be shielded by UV-blocking soft contact lenses. Sunglasses may be unable to shield oblique rays, unless side protection is incorporated. Contact lenses can offer UVR protection against all angles of incidence, including the peak-response angle. They can also protect the eye in settings in which the wearing of sunglasses is not feasible or convenient.

Contact Lenses↗
PubMed2006

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

BACKGROUND: There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl. RESULTS: The measure of prediction success is greatly affected by the level of imbalance in the training dataset. We found the balanced dataset that included all attributes produced the best prediction. The performance as measured by the Matthews correlation coefficient (MCC) varied between 0.49 and 0.25 depending on the imbalance. As previously observed, the degree of sequence conservation at the nsSNP position is the single most useful attribute. In addition to conservation, structural predictions made using a balanced dataset can be of value. CONCLUSION: The predictions for all nsSNPs within Ensembl, based on a balanced dataset using all attributes, are available as a DAS annotation. Instructions for adding the track to Ensembl are at http://www.brightstudy.ac.uk/das_help.html.

Algorithms↗
PubMed2006

A third approach to gene prediction suggests thousands of additional human transcribed regions.

The identification and characterization of the complete ensemble of genes is a main goal of deciphering the digital information stored in the human genome. Many algorithms for computational gene prediction have been described, ultimately derived from two basic concepts: (1) modeling gene structure and (2) recognizing sequence similarity. Successful hybrid methods combining these two concepts have also been developed. We present a third orthogonal approach to gene prediction, based on detecting the genomic signatures of transcription, accumulated over evolutionary time. We discuss four algorithms based on this third concept: Greens and CHOWDER, which quantify mutational strand biases caused by transcription-coupled DNA repair, and ROAST and PASTA, which are based on strand-specific selection against polyadenylation signals. We combined these algorithms into an integrated method called FEAST, which we used to predict the location and orientation of thousands of putative transcription units not overlapping known genes. Many of the newly predicted transcriptional units do not appear to code for proteins. The new algorithms are particularly apt at detecting genes with long introns and lacking sequence conservation. They therefore complement existing gene prediction methods and will help identify functional transcripts within many apparent "genomic deserts."

Algorithms↗